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Sample records for complex crystal structures

  1. Amine free crystal structure: The crystal structure of d(CGCGCG)2 and methylamine complex crystal

    International Nuclear Information System (INIS)

    Ohishi, Hirofumi; Tsukamoto, Koji; Hiyama, Yoichi; Maezaki, Naoyoshi; Tanaka, Tetsuaki; Ishida, Toshimasa

    2006-01-01

    We succeeded in the crystallization of d(CGCGCG) 2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2F o - F c map was much clear and easily traced. It is First time monoamine co-crystallizes with d(CGCGCG) 2 . However, methylamine was not found from the complex crystal of d(CGCGCG) 2 and methylamine. Five Mg ions were found around d(CGCGCG) 2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg 2+ . DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG) 2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this

  2. Photonic crystals, light manipulation, and imaging in complex nematic structures

    Science.gov (United States)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  3. Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

    KAUST Repository

    Dumbrack, Roland

    2016-01-26

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

  4. Synthesis and crystal structure of two lead (II) complexes with 1,10-phenanthroline ligand

    International Nuclear Information System (INIS)

    Olivera, Fiorella L.; Santillan, Guillermo A.

    2012-01-01

    Two coordination complexes have been synthesized by the reaction of lead nitrate (II) with 1,10-phenanthroline in methanol/water. The crystals of these complexes were obtained by using the diffusion method and structurally characterized by X-ray single crystal diffraction. Both complexes crystallized in the monoclinic space group P2 1 /c. The analysis by crystal X-ray diffraction reveals that in both complexes the coordination around the lead (II) ion is a distorted octahedral structure where the ion is bonded to the heterocyclic nitrogen atoms of chelating ligand 1,10-phenanthroline, three oxygen atoms of three nitrate groups and one oxygen from the water molecule. The difference between the complexes lies in the way of nitrate ion in presence of carboxylic acid aromatics. In addition, the crystal structure of complexes can be regarded as a 3D coordination polymer through Pb-O weak interactions, hydrogen bonds and π-π stacking interactions. (author).

  5. Crystal structure of Sus scrofa quinolinate phosphoribosyltransferase in complex with nicotinate mononucleotide.

    Directory of Open Access Journals (Sweden)

    Hyung-Seop Youn

    Full Text Available We have determined the crystal structure of porcine quinolinate phosphoribosyltransferase (QAPRTase in complex with nicotinate mononucleotide (NAMN, which is the first crystal structure of a mammalian QAPRTase with its reaction product. The structure was determined from protein obtained from the porcine kidney. Because the full protein sequence of porcine QAPRTase was not available in either protein or nucleotide databases, cDNA was synthesized using reverse transcriptase-polymerase chain reaction to determine the porcine QAPRTase amino acid sequence. The crystal structure revealed that porcine QAPRTases have a hexameric structure that is similar to other eukaryotic QAPRTases, such as the human and yeast enzymes. However, the interaction between NAMN and porcine QAPRTase was different from the interaction found in prokaryotic enzymes, such as those of Helicobacter pylori and Mycobacterium tuberculosis. The crystal structure of porcine QAPRTase in complex with NAMN provides a structural framework for understanding the unique properties of the mammalian QAPRTase active site and designing new antibiotics that are selective for the QAPRTases of pathogenic bacteria, such as H. pylori and M. tuberculosis.

  6. Origin of the complex crystal structures of elements at intermediate pressure

    International Nuclear Information System (INIS)

    Ackland, G J; Macleod, I R

    2004-01-01

    We present a unifying theory for the observed complex structures of sp-bonded elements under pressure on the basis of nearly free electron picture. In the intermediate pressure regime, the dominant contribution to crystal structure arises from Fermi-surface Brillouin zone interactions-structures which allow this are favoured. This simple theory explains the observed crystal structures, transport properties and the evolution of internal and unit cell parameters with pressure and appears to hold for elements in groups I-VI. We illustrate it with experimental data for these elements and ab initio calculations for Li

  7. Crystallization and preliminary X-ray structural studies of a Melan-A pMHC–TCR complex

    International Nuclear Information System (INIS)

    Yuan, Fang; Georgiou, Theonie; Hillon, Theresa; Gostick, Emma; Price, David A.; Sewell, Andrew K.; Moysey, Ruth; Gavarret, Jessie; Vuidepot, Annelise; Sami, Malkit; Bell, John I.; Gao, George F.; Rizkallah, Pierre J.; Jakobsen, Bent K.

    2007-01-01

    A preliminary X-ray crystal structural study of a soluble cognate T-cell receptor (TCR) in complex with a pMHC presenting the Melan-A peptide (ELAGIGILTV) is reported. The TCR and pMHC were refolded, purified and mixed together to form complexes, which were crystallized using the sitting-drop vapour-diffusion method. Single TCR–pMHC complex crystals were cryocooled and used for data collection. Melanocytes are specialized pigmented cells that are found in all healthy skin tissue. In certain individuals, diseased melanocytes can form malignant tumours, melanomas, which cause the majority of skin-cancer-related deaths. The melanoma-associated antigenic peptides are presented on cell surfaces via the class I major histocompatibility complex (MHC). Among the melanoma-associated antigens, the melanoma self-antigen A/melanoma antigen recognized by T cells (Melan-A/MART-1) has attracted attention because of its wide expression in primary and metastatic melanomas. Here, a preliminary X-ray crystal structural study of a soluble cognate T-cell receptor (TCR) in complex with a pMHC presenting the Melan-A peptide (ELAGIGILTV) is reported. The TCR and pMHC were refolded, purified and mixed together to form complexes, which were crystallized using the sitting-drop vapour-diffusion method. Single TCR–pMHC complex crystals were cryocooled and used for data collection. Diffraction data showed that these crystals belonged to space group P4 1 /P4 3 , with unit-cell parameters a = b = 120.4, c = 81.6 Å. A complete data set was collected to 3.1 Å and the structure is currently being analysed

  8. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

    Science.gov (United States)

    Xu, Qifang; Malecka, Kimberly L.; Fink, Lauren; Jordan, E. Joseph; Duffy, Erin; Kolander, Samuel; Peterson, Jeffrey; Dunbrack, Roland L.

    2016-01-01

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an “autophosphorylation complex.” We developed and applied a structural bioinformatics method to identify all such autophosphorylation kinase complexes in X-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which 5 complexes had not previously been described in the publications describing the crystal structures. These 5 consist of tyrosine residues in the N-terminal juxtamembrane regions of colony stimulating factor 1 receptor (CSF1R, Tyr561) and EPH receptor A2 (EPHA2, Tyr594), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr394) and insulin-like growth factor 1 receptor (IGF1R, Tyr1166), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser142). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro447 to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets. PMID:26628682

  9. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  10. Synthesis, Crystal Structure of a Novel Mn Complex with Nicotinoyl-Glycine

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    Xin Wang

    2016-12-01

    Full Text Available A novel manganese complex, C16H26MnN4O12, was synthesized by the reaction of nicotinoyl-glycine and NaOH in an ethanol/water solution and structurally characterized by elemental analysis, UV-vis spectrum, IR spectrum and single-crystal X-ray diffraction analysis. The crystal of the complex belongs to the triclinic space group P1 with a = 7.8192(16 Å, b = 8.8800(18 Å, c = 9.0142(18 Å, α = 83.14(3°, β = 65.27(3°, γ = 81.67(3°, V = 516.3(2 Å3, Z = 1, Dx = 1.542 mg·m−3, μ = 0.66 mm−1, F(000 = 271, and final R1 = 0.0381, ωR2 = 0.0964. The nicotinoyl-glycine ligand acts as a bridging ligand to connect the manganese ions by the hydrogen interactions; thus, the complex expands into a 3D supramolecular net structure.

  11. Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

    OpenAIRE

    Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

    1981-01-01

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

  12. Crystal Structure of an L-Carnitine Complex with Pyrogallol[4]arene

    International Nuclear Information System (INIS)

    Fujisawa, I; Takeuchi, D; Kitamura, Y; Okamoto, R; Aoki, K

    2012-01-01

    L-Carnitine is essential for the transport of long-chain fatty acids from cytosol into mitochondria for generating metabolic energy. The survey of crystal structures of carnitine-containing proteins in the Protein Data Bank reveals that carnitine can take several conformations with the quarternary trimethylammonium terminal being always bound to aromatic residues through cation-π interactions in acyltransferases or carnitine-binding proteins. In order to demonstrate the importance of cation-π interaction as a carnitine recognition mechanism in the artificial receptor-ligand system that mimics the carnitine-binding sites, we have determined the crystal structure of a complex formed between L-carnitine and pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT) as a carnitine receptor, 2PCT·2(L-carnitine)·4EtOH. There form two crystallographically independent monomeric [PCT·L-carnitine] substructures, which further form an obliquely arranged capsule-like dimeric [PCT·L-carnitine] 2 structure through a pair of O-H (PCT)···O (L-carnitine) hydrogen bonds. This is the first report of PCT complex with chiral molecules. In each of the two monomeric [PCT·L-carnitine] substructures, the L-carnitine molecule takes the elongated form with an intramolecular hydrogen bond between the hydroxyl group and the carboxylate oxygen, and the cationic trimethylammonium moiety is incorporated into the cavity of the bowl-shaped PCT molecule through cation-π interactions. These features are similar to those at the D-carnitine-binding site in the crystal structure of the glycine betaine/carnitine/choline-binding protein complex.

  13. Crystal structure of the human 4-1BB/4-1BBL complex.

    Science.gov (United States)

    Gilbreth, Ryan N; Oganesyan, Vaheh Y; Amdouni, Hamza; Novarra, Shabazz; Grinberg, Luba; Barnes, Arnita; Baca, Manuel

    2018-05-02

    4-1BBL is a member of the TNF superfamily and is the ligand for the TNFRsuperfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells and agonists of this receptor have garnered strong attention as potentialimmunotherapy agents. Broadly speaking, the structural features of TNF superfamilymembers, their receptors and ligand/receptor complexes are similar. However, apublished crystal structure of human 4-1BBL suggests that it may be unique in thisregard, exhibiting a three-bladed propeller-like trimer assembly that is distinctly different from that observed in other family members. This unusual structure also suggests that the human 4-1BB/4-1BBL complex may be structurally unique within the TNF/TNFR superfamily, but to date no structural data have been reported. Here we report the crystal structure of the human 4-1BB/4-1BBL complex at 2.4 Å resolution. In this structure, 4-1BBL does not adopt the unusual trimer assembly previously reported, but instead forms a canonical bell-shaped trimer typical of other TNF superfamily members. The structure of 4-1BB is also largely canonical as is the 4-1BB/4-1BBL complex. Mutational data support the 4-1BBL structure reported here as being biologically relevant, suggesting that the previously reported structure is not. Together, the data presented here offer insight into structure/function relationships in the 4-1BB/4-1BBL system and improve our structural understanding of the TNF/TNFR superfamily more broadly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Crystal structure of the β2 adrenergic receptor-Gs protein complex

    DEFF Research Database (Denmark)

    Rasmussen, Søren Gøgsig Faarup; DeVree, Brian T; Zou, Yaozhong

    2011-01-01

    -occupied receptor. The β(2) adrenergic receptor (β(2)AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β(2)AR and nucleotide-free Gs...

  15. Synthesis, crystal structure and applications of palladium thiosalicylate complexes

    Directory of Open Access Journals (Sweden)

    S.B. Moosun

    2017-05-01

    Full Text Available Three palladium thiosalicylate complexes [Pd(tb(bipy]·3H2O (1, [Pd2(tb2(bipy2]·(dtdb2 (2 and [Pd2(tb2(phen2]·dtdb·H2O (3 (bipy = bipyridine; phen = phenanthroline were prepared from the reaction of PdCl2(CH3CN2 with dithiosalicylic acid (dtdb which underwent cleavage to form thiobenzoate anion (tb in DMF/MeOH. Square planar geometries of the complexes with a N2SO coordination type were proposed on the basis of single crystal X-ray structural study. The presence of trapped and uncoordinated dtdb was observed in complexes 2 and 3. Complexes 1–3 were evaluated as catalysts for Heck coupling reactions of methyl acrylate with iodobenzene, and showed moderate activities at a very low catalyst loading. Complex 1 was found to inhibit the growth of bacteria and scavenge free radicals efficiently.

  16. Introduction to crystal structure determination methods using x-ray diffraction: application to some rare earth complexes

    International Nuclear Information System (INIS)

    Oliveira, M.A. de.

    1986-01-01

    This work is composed by a theoretical introduction studying crystal concept, interaction between X-ray and crystal medium, and methods for determining small molecular structures applied in solution of crystal structures of praseodymium, neodymium and europium complexes with perrhenate and trans - 1,4 - dithiane - 1,4 - dioxide, (TDTD), which general formula is [ Ln (H sub(2) O) sub(4) (η-TDTD) (η'Re O sub(4)) (μ-η sup(2)-TDTD)] sub(n) (Re O sub(4)) sub(2n). nTDTD, where, Ln = Eu, Pr, Nd and methyl-2,6-anhydrous-3-azido-4-0-benzoyl-3-deoxy-α-D-iodo pyranoside. The structure of C sub(14) H sub(15) N sub(3) O sub(5) organic complex was determined using direct methods. (M.C.K.)

  17. Crystallization of protein–ligand complexes

    International Nuclear Information System (INIS)

    Hassell, Anne M.; An, Gang; Bledsoe, Randy K.; Bynum, Jane M.; Carter, H. Luke III; Deng, Su-Jun J.; Gampe, Robert T.; Grisard, Tamara E.; Madauss, Kevin P.; Nolte, Robert T.; Rocque, Warren J.; Wang, Liping; Weaver, Kurt L.; Williams, Shawn P.; Wisely, G. Bruce; Xu, Robert; Shewchuk, Lisa M.

    2007-01-01

    Methods presented for growing protein–ligand complexes fall into the categories of co-expression of the protein with the ligands of interest, use of the ligands during protein purification, cocrystallization and soaking the ligands into existing crystals. Obtaining diffraction-quality crystals has long been a bottleneck in solving the three-dimensional structures of proteins. Often proteins may be stabilized when they are complexed with a substrate, nucleic acid, cofactor or small molecule. These ligands, on the other hand, have the potential to induce significant conformational changes to the protein and ab initio screening may be required to find a new crystal form. This paper presents an overview of strategies in the following areas for obtaining crystals of protein–ligand complexes: (i) co-expression of the protein with the ligands of interest, (ii) use of the ligands during protein purification, (iii) cocrystallization and (iv) soaks

  18. Zinc(II) complexes of carboxamide derivatives: Crystal structures ...

    Indian Academy of Sciences (India)

    can form complexes with a variety of metal ions. Recently, bi- ... tural analyses of both ligands and complex 1 by single crystal X-ray ..... software over a Red Hat Linux IBM cluster using den- .... Change in the relative viscosity (η/ηo)1/3 of CT-.

  19. Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

    Science.gov (United States)

    Chumakov, Yu. M.; Tsapkov, V. I.; Jeanneau, E.; Bairac, N. N.; Bocelli, G.; Poirier, D.; Roy, J.; Gulea, A. P.

    2008-09-01

    The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate ( I), bromo-(2-formylpyridinethiosemicarbazono)copper ( II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate ( III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I III at a concentration of 10-5 mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

  20. Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

    International Nuclear Information System (INIS)

    Chumakov, Yu. M.; Tsapkov, V. I.; Jeanneau, E.; Bairac, N. N.; Bocelli, G.; Poirier, D.; Roy, J.; Gulea, A. P.

    2008-01-01

    The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate (I), bromo-(2-formylpyridinethiosemicarbazono)copper (II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate (III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I-III at a concentration of 10 -5 mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

  1. Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

    Energy Technology Data Exchange (ETDEWEB)

    Chumakov, Yu. M., E-mail: chumakov.xray@phys.asm.md [Academy of Sciences of Moldova, Institute of Applied Physics (Moldova, Republic of); Tsapkov, V. I. [State University of Moldova (Moldova, Republic of); Jeanneau, E. [Universite Claude Bernard, Laboratoire des Multimateriaux et Interfaces (France); Bairac, N. N. [State University of Moldova (Moldova, Republic of); Bocelli, G. [National Research Council (IMEM-CNR), Institute of Materials for Electronics and Magnetism (Italy); Poirier, D.; Roy, J. [Centre Hospitalier Universitaire de Quebec (CHUQ) (Canada); Gulea, A. P. [State University of Moldova (Moldova, Republic of)

    2008-09-15

    The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate (I), bromo-(2-formylpyridinethiosemicarbazono)copper (II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate (III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I-III at a concentration of 10{sup -5} mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

  2. Crystal Structures of Murine Carnitine Acetyltransferase in Ternary Complexes with Its Substrates

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao,Y.; Jogl, G.; Tong, L.

    2006-01-01

    Carnitine acyltransferases catalyze the reversible exchange of acyl groups between coenzyme A (CoA) and carnitine. They have important roles in many cellular processes, especially the oxidation of long-chain fatty acids in the mitochondria for energy production, and are attractive targets for drug discovery against diabetes and obesity. To help define in molecular detail the catalytic mechanism of these enzymes, we report here the high resolution crystal structure of wild-type murine carnitine acetyltransferase (CrAT) in a ternary complex with its substrates acetyl-CoA and carnitine, and the structure of the S554A/M564G double mutant in a ternary complex with the substrates CoA and hexanoylcarnitine. Detailed analyses suggest that these structures may be good mimics for the Michaelis complexes for the forward and reverse reactions of the enzyme, representing the first time that such complexes of CrAT have been studied in molecular detail. The structural information provides significant new insights into the catalytic mechanism of CrAT and possibly carnitine acyltransferases in general.

  3. Crystal Structure of the Herpesvirus Nuclear Egress Complex Provides Insights into Inner Nuclear Membrane Remodeling

    Directory of Open Access Journals (Sweden)

    Tzviya Zeev-Ben-Mordehai

    2015-12-01

    Full Text Available Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus proteins pUL31 and pUL34 form the heterodimeric nuclear egress complex (NEC, which, in turn, mediates the formation of tight-fitting membrane vesicles around capsids at the inner nuclear membrane. Here, we present the crystal structure of the pseudorabies virus NEC. The structure revealed that a zinc finger motif in pUL31 and an extensive interaction network between the two proteins stabilize the complex. Comprehensive mutational analyses, characterized both in situ and in vitro, indicated that the interaction network is not redundant but rather complementary. Fitting of the NEC crystal structure into the recently determined cryoEM-derived hexagonal lattice, formed in situ by pUL31 and pUL34, provided details on the molecular basis of NEC coat formation and inner nuclear membrane remodeling.

  4. Crystal and Molecular Structure of Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II Complex

    Directory of Open Access Journals (Sweden)

    Hakan Arslan

    2011-01-01

    Full Text Available Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II complex has been synthesized and characterized by elemental analysis and FT-IR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, with a = 13.046(2 Å, b = 13.135(2 Å, c = 13.179(2 Å, α= 67.083(4°, β= 67.968(4°, γ = 84.756(4° and Dcalc =1.330 g/cm3 for Z = 2. The crystal structure confirms that the complex is a mononuclear copper(II complex and the 2,2-diphenyl-N-(di-n-propyl-carbamothioylacetamide ligand is a bidentate chelating ligand, coordinating to the copper atom through the thiocarbonyl and carbonyl groups. This coordination has a slightly distorted square-planar geometry (O1-Cu1-O2: 86.48(11°, O1-Cu1-S1: 93.85(9°, O2-Cu1-S2: 94.20(9° and S1-Cu1-S2: 91.21(4°. The title molecule shows a cis-arrangement and C–O, C–S and C–N bond lengths of the complex suggest considerable electronic delocalization in the chelate rings.

  5. Triboluminescence and crystal structure of the complex [Eu(NО3 )3 (HMPA)3 ]: role of cleavage planes.

    Science.gov (United States)

    Bukvetskii, B V; Mirochnik, A G; Zhikhareva, P A

    2017-05-01

    The atomic structure of crystals of the [Eu(NО 3 ) 3 (HMPA) 3 ] [hexamethylphosphotriamide (HMPA)] complex characterized by an intensive luminescence and triboluminescence was determined using X-ray structural analysis. Noncentrosymmetric crystals have a monoclinic syngony: a = 16.0686 (3), b = 11.0853 (2), c = 20.9655 Å (4), β = 93.232° (1), space group P2 1 , Z = 4, ρ calc  = 1.560 g/cm 3 . The crystal structure is represented by individual С 18 Н 54 EuN 12 O 12 P 3 complexes linked through van der Waals interactions with clearly expressed cleavage planes. The Eu(III) atom coordination polyhedron reflected the state of a distorted square antiprism. Structural aspects of the suggested model, including formation of triboluminescence properties, were considered and the role of the cleavage planes was discussed. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline–3-hydroxy-4-methoxybenzaldehyde

    International Nuclear Information System (INIS)

    Sharma, K.P.; Reddi, R.S.B.; Bhattacharya, S.; Rai, R.N.

    2012-01-01

    The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV–Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied. - Graphical abstarct: Exploiting phase diagram study and solvent free synthesis a novel compound was synthesized and its single crystal growth, atomic packing, energy band gap and refractive index were studied. Highlights: ► Novel organic complex was synthesized using Green or solvent free synthesis. ► Phase diagram study provided the information to identify the worthy composition of novel complex. ► The single crystal of the sufficient size was grown from the ethanol solution. ► Crystal analysis suggested that the covalent bond is formed between the two parent compounds. ► The transmittance of the crystal was found to be 70% and it was transparent from 412 to 850 nm.

  7. 1D cyanide complexes with 2-pyridinemethanol: Synthesis, crystal structures and spectroscopic properties

    Science.gov (United States)

    Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

    2015-12-01

    Two new one-dimensional coordination polymers, [Cu(hmpH)2Pd(μ-CN)2(CN)2]n (1) and [Cu(hmpH)2Pt(μ-CN)2(CN)2]n (2), (hmpH = 2-pyridinemethanol), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. Single crystal X-ray diffraction analysis indicates that complexes 1 and 2 are isomorphous and isostructural, and crystallize in the triclinic system and P-1 space group. The Pd(II) or Pt(II) ions are four coordinated with four cyanide-carbon atoms in a square planar geometry. Cu(II) ion displays a distorted octahedral coordination by two N-atoms and two O-atoms of hmpH ligands, two bridging cyanide groups. In one dimensional structure of the complexes, [M(CN)4]2- (M = Pd(II) or Pt(II)) anions and [Cu(hmpH)2]2+ cations are linked via bridging cyanide ligands. In the complexes, the presence of intramolecular C-H⋯M (M = Pd(II) or Pt(II)) interactions with distance values of 3.00-2.95 Å are established, respectively.

  8. Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline-3-hydroxy-4-methoxybenzaldehyde

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, K.P.; Reddi, R.S.B.; Bhattacharya, S. [Department of Chemistry, Centre of Advance Study, Banaras Hindu University, Varanasi-221005 (India); Rai, R.N., E-mail: rn_rai@yahoo.co.in [Department of Chemistry, Centre of Advance Study, Banaras Hindu University, Varanasi-221005 (India)

    2012-06-15

    The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV-Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied. - Graphical abstarct: Exploiting phase diagram study and solvent free synthesis a novel compound was synthesized and its single crystal growth, atomic packing, energy band gap and refractive index were studied. Highlights: Black-Right-Pointing-Pointer Novel organic complex was synthesized using Green or solvent free synthesis. Black-Right-Pointing-Pointer Phase diagram study provided the information to identify the worthy composition of novel complex. Black-Right-Pointing-Pointer The single crystal of the sufficient size was grown from the ethanol solution. Black-Right-Pointing-Pointer Crystal analysis suggested that the covalent bond is formed between the two parent compounds. Black-Right-Pointing-Pointer The transmittance of the crystal was found to be 70% and it was transparent from 412 to 850 nm.

  9. Colorimetric detection of hydrogen peroxide by dioxido-vanadium(V) complex containing hydrazone ligand: synthesis and crystal structure

    Science.gov (United States)

    Kurbah, Sunshine D.; Syiemlieh, Ibanphylla; Lal, Ram A.

    2018-03-01

    Dioxido-vanadium(V) complex has been synthesized in good yield, the complex was characterized by IR, UV-visible and 1H NMR spectroscopy. Single crystal X-ray crystallography techniques were used to assign the structure of the complex. Complex crystallized with monoclinic P21/c space group with cell parameters a (Å) = 39.516(5), b (Å) = 6.2571(11), c (Å) = 17.424(2), α (°) = 90, β (°) = 102.668(12) and γ (°) = 90. The hydrazone ligand is coordinate to metal ion in tridentate fashion through -ONO- donor atoms forming a distorted square pyramidal geometry around the metal ion.

  10. Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies

    Energy Technology Data Exchange (ETDEWEB)

    AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio; Egea, Pascal F.

    2017-06-01

    Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.

  11. Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

    Science.gov (United States)

    Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

    1981-08-04

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

  12. Hydrothermal synthesis, crystal structure, luminescent and magnetic properties of a new mononuclear GdIII coordination complex

    Science.gov (United States)

    Coban, Mustafa Burak

    2018-06-01

    A new GdIII coordination complex, {[Gd(2-stp)2(H2O)6].2(4,4'-bipy).4(H2O)}, complex 1, (2-stp = 2-sulfoterephthalate anion and 4,4'-bipy = 4,4'-bipyridine), has been synthesized by hydrothermal method and characterized by elemental analysis, solid state UV-Vis and FT-IR spectroscopy, single-crystal X-ray diffraction, solid state photoluminescence and variable-temperature magnetic measurements. The crystal structure determination shows that GdIII ions are eight coordinated and adopt a distorted square-antiprismatic geometry. Molecules interacting through intra- and intermolecular (O-H⋯O, O-H⋯N) hydrogen bonds in complex 1, give rise to 3D hydrogen bonded structure and the discrete lattice 4,4'-bipy molecules occupy the channel of the 3D structure. π-π stacking interactions also exist 4,4'-bipy-4,4'-bipy and 4,4'-bipy-2-stp molecule rings in 3D structures. Additionally, solid state photoluminescence properties of complex 1 at room temperature have been investigated. Under the excitation of UV light (at 349 nm), the complex 1 exhibited green emissions (at 505 nm) of GdIII ion in the visible region. Furthermore, Variable-temperature magnetic susceptibility and isothermal magnetization as function of external magnetic field studies reveal that complex 1 displays possible antiferromagnetic interaction.

  13. A mononuclear zinc(II) complex with piroxicam: Crystal structure, DNA- and BSA-binding studies; in vitro cell cytotoxicity and molecular modeling of oxicam complexes

    Science.gov (United States)

    Jannesari, Zahra; Hadadzadeh, Hassan; Amirghofran, Zahra; Simpson, Jim; Khayamian, Taghi; Maleki, Batool

    2015-02-01

    A new mononuclear Zn(II) complex, trans-[Zn(Pir)2(DMSO)2], where Pir- is 4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (piroxicam), has been synthesized and characterized. The crystal structure of the complex was obtained by the single crystal X-ray diffraction technique. The interaction of the complex with DNA and BSA was investigated. The complex interacts with FS-DNA by two binding modes, viz., electrostatic and groove binding (major and minor). The microenvironment and the secondary structure of BSA are changed in the presence of the complex. The anticancer effects of the seven complexes of oxicam family were also determined on the human K562 cell lines and the results showed reasonable cytotoxicities. The interactions of the oxicam complexes with BSA and DNA were modeled by molecular docking and molecular dynamic simulation methods.

  14. Synthesis and X-Ray Crystal Structures of Mononuclear Complexes of 1,3-Bis(8-quinolyloxy)propane

    International Nuclear Information System (INIS)

    Al-Mandhary, M.R.; Steel, P.

    2002-01-01

    The preparations and X-ray crystal structures of the first transition metal complexes of 1,3-bis(8-quinolyloxy)propane are described. The ligand acts as a trans-chelating N,N'-bidentate ligand in the three-coordinate silver nitrate complex and four-coordinate copper chloride complex, but as an N,O,O',N'-tetradentate ligand in the octahedral nickel chloride complex. Copyright (2002) CSIRO Australia

  15. Crystallization of bi-functional ligand protein complexes.

    Science.gov (United States)

    Antoni, Claudia; Vera, Laura; Devel, Laurent; Catalani, Maria Pia; Czarny, Bertrand; Cassar-Lajeunesse, Evelyn; Nuti, Elisa; Rossello, Armando; Dive, Vincent; Stura, Enrico Adriano

    2013-06-01

    Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

    Science.gov (United States)

    Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

    2010-08-14

    Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

  17. The Crystal Structures of Two Novel Cadmium-Picolinic Acid ...

    African Journals Online (AJOL)

    The crystal structures of two novel cadmium-picolinic acid complexes grown in aqueous solutions at selected pH values are reported. The structures are compared to expected solution species under the same conditions. The crystal structure of complex 1 exhibits a seven coordinate structure which contains a protonated ...

  18. Crystal structures of bromo- and iododerivatives of ruthenium nitroso complexes K2[RuNOX5

    International Nuclear Information System (INIS)

    Mikhajlov, Yu.N.; Kanishcheva, A.S.; Svetlov, A.A.

    1989-01-01

    Method of X-ray diffraction analysis was used to interpret crystal structure of ruthenium pentahalogenonitroso complexes: K 2 [RuNOBr 5 ] (1) and K 2 [RuOI 5 ] (2). Crystals belong to rhombic syngony, sp.gr. Pcmn. Lattice parameters: (1) - a 7.236(2), b = 10.791(2), c = 13.949(3) A, V = 1089.14(1) A 3 , Z = 4; (2) - a = 7.755(1), b = 11.506(6), c = 14.951(5) A, V 133.97(8) A 3 , Z = 4. It was revealed that lengths of Ru-Br equatorial bonds in (1) exceeded the axial ones, and in the compound (2) the reverse relation was observed. The obtained results were correlated with the structural data for K 2 [RuNOF 5 ]H 2 O and K 2 [RuNOCl 5 ] complexes and similar osmium compounds

  19. Zinc(II) halide complexes with 2-methoxyaniline ligand: Synthesis, characterization, thermal analyses, crystal structure determination and luminescent properties

    Science.gov (United States)

    Amani, Vahid

    2018-03-01

    Three new mononuclear zinc(II) complexes, [Zn(2-MeO-C6H4NH2)2X2] (X is Cl in 1, Br in 2 and I in 3), were prepared from the reactions of ZnX2 with 2-methoxyaniline (2-MeO-C6H4NH2) ligand in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurements by slow evaporation of methanol solution at room temperature. The three complexes were thoroughly characterized by thermogravimetric analysis, elemental analysis (CHNO), spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the zinc(II) cation is four-coordinated in a distorted tetrahedral configuration by two N atoms from two 2-methoxyanyline ligands and two halide anions. Also, in these complexes intermolecular interactions, for example Nsbnd H⋯X hydrogen bonds (in 1-3), Csbnd H⋯X hydrogen bonds (in 3), Csbnd H⋯π interactions (in 1 and 2) and π⋯π interactions (in 3), are effective in the stabilization of the crystal structures. In addition, the luminescence spectra of all complexes in methanolic solution show that the intensity of their emission bands is stronger than that for free 2-methoxyaniline ligand.

  20. Crystallization, data collection and processing of the chymotrypsin–BTCI–trypsin ternary complex

    Energy Technology Data Exchange (ETDEWEB)

    Esteves, Gisele Ferreira; Teles, Rozeni Chagas Lima; Cavalcante, Nayara Silva; Neves, David; Ventura, Manuel Mateus [Laboratório de Biofísica, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900 Brasília-DF (Brazil); Barbosa, João Alexandre Ribeiro Gonçalves, E-mail: joao@lnls.br [Center for Structural Molecular Biology (CeBiME), Brazilian Synchrotron Light Laboratory (LNLS), CP 6192, 13083-970 Campinas-SP (Brazil); Freitas, Sonia Maria de, E-mail: joao@lnls.br [Laboratório de Biofísica, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900 Brasília-DF (Brazil)

    2007-12-01

    A ternary complex of the proteinase inhibitor (BTCI) with trypsin and chymotrypsin was crystallized and its crystal structure was solved by molecular replacement. A ternary complex of the black-eyed pea trypsin and chymotrypsin inhibitor (BTCI) with trypsin and chymotrypsin was crystallized by the sitting-drop vapour-diffusion method with 0.1 M HEPES pH 7.5, 10%(w/v) polyethylene glycol 6000 and 5%(v/v) 2-methyl-2,4-pentanediol as precipitant. BTCI is a small protein with 83 amino-acid residues isolated from Vigna unguiculata seeds and is able to inhibit trypsin and chymotrypsin simultaneously by forming a stable ternary complex. X-ray data were collected from a single crystal of the trypsin–BTCI–chymotrypsin ternary complex to 2.7 Å resolution under cryogenic conditions. The structure of the ternary complex was solved by molecular replacement using the crystal structures of the BTCI–trypsin binary complex (PDB code) and chymotrypsin (PDB code) as search models.

  1. Crystallization, data collection and processing of the chymotrypsin–BTCI–trypsin ternary complex

    International Nuclear Information System (INIS)

    Esteves, Gisele Ferreira; Teles, Rozeni Chagas Lima; Cavalcante, Nayara Silva; Neves, David; Ventura, Manuel Mateus; Barbosa, João Alexandre Ribeiro Gonçalves; Freitas, Sonia Maria de

    2007-01-01

    A ternary complex of the proteinase inhibitor (BTCI) with trypsin and chymotrypsin was crystallized and its crystal structure was solved by molecular replacement. A ternary complex of the black-eyed pea trypsin and chymotrypsin inhibitor (BTCI) with trypsin and chymotrypsin was crystallized by the sitting-drop vapour-diffusion method with 0.1 M HEPES pH 7.5, 10%(w/v) polyethylene glycol 6000 and 5%(v/v) 2-methyl-2,4-pentanediol as precipitant. BTCI is a small protein with 83 amino-acid residues isolated from Vigna unguiculata seeds and is able to inhibit trypsin and chymotrypsin simultaneously by forming a stable ternary complex. X-ray data were collected from a single crystal of the trypsin–BTCI–chymotrypsin ternary complex to 2.7 Å resolution under cryogenic conditions. The structure of the ternary complex was solved by molecular replacement using the crystal structures of the BTCI–trypsin binary complex (PDB code) and chymotrypsin (PDB code) as search models

  2. Low-dimensional compounds containing cyanido groups. XXVIII. Crystal structure, spectroscopic and magnetic properties of two copper(II) tetracyanidoplatinate complexes with 1,2-diaminopropane

    International Nuclear Information System (INIS)

    Vavra, Martin; Potočňák, Ivan; Dušek, Michal; Čižmár, Erik; Ozerov, Mykhaylo; Zvyagin, Sergei A.

    2015-01-01

    Violet crystals of ([Cu(pn) 2 ] 2 [Pt(CN) 4 ])[Pt(CN) 4 ]·2H 2 O (1, pn=1,2-diaminopropane) and blue crystals of [Cu(pn)Pt(CN) 4 ] n ·nH 2 O (2) were prepared under hydrothermal conditions and characterized using elemental analysis, IR and UV–vis spectroscopy and by X-ray crystal structure analysis. Different number of ν(C≡N) absorption bands of these two compounds reflects their different structures. An X-ray crystal structure analysis has shown that complex 1 is of ionic character and is formed from trinuclear [Cu(pn) 2 –Pt(CN) 4 –Cu(pn) 2 ] 2+ complex cation and discrete [Pt(CN) 4 ] 2– anion together with two molecules of crystal water. On the other hand, complex 2 is of polymeric character and is formed by 2D networks of [Cu(pn)Pt(CN) 4 ] n composition and completed by n molecules of crystal water. Magnetic measurements show the presence of a weak antiferromagnetic exchange interaction in complex 1 (Θ=–0.2 K), while the magnetic susceptibility of complex 2 is well described by the model of uniform S=1/2 spin chain with exchange interaction J/k B =–1.64 K. - Graphical abstract: Two complexes of different structural types from the system Cu(II) – 1,2–diaminopropane – [Pt(CN) 4 ] 2– have been isolated. These were characterized by IR and UV–VIS spectroscopy, X–ray crystal structure analysis together with the magnetic measurements. On one hand ([Cu(pn) 2 ] 2 [Pt(CN) 4 ])[Pt(CN) 4 ]∙2H 2 O is of ionic character and is formed from trinuclear complex cation and discrete anion together with two molecules of crystal water. On the other hand, [Cu(pn)Pt(CN) 4 ] n ∙nH 2 O is of polymeric character and is formed by 2D networks of [Cu(pn)Pt(CN) 4 ] n composition and completed by n molecules of crystal water. - Highlights: • Two complexes of different compositions from one system have been isolated. • First complex is of ionic character and second one is of polymeric character. • Polymeric complex described as a spin chain in contrast to

  3. Crystal Structure of the VapBC Toxin–Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly

    DEFF Research Database (Denmark)

    Dienemann, Christian; Bøggild, Andreas; Winther, Kristoffer S.

    2011-01-01

    the crystal structure of the intact Shigella flexneri VapBC TA complex, determined to 2.7 Å resolution. Both in solution and in the crystal structure, four molecules of each protein combine to form a large and globular hetero-octameric assembly with SpoVT/AbrB-type DNA-binding domains at each end and a total...

  4. Crystal structure of the Copper(I) complex Cu(py-Clan)(PPh.sub.3./sub.)I

    Czech Academy of Sciences Publication Activity Database

    Khalaji, A.D.; Jafari, K.; Fejfarová, Karla; Dušek, Michal

    2015-01-01

    Roč. 56, č. 1 (2015), s. 175-178 ISSN 0022-4766 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : copper(I) complex * Schiff base * crystal structure Subject RIV: CC - Organic Chemistry Impact factor: 0.536, year: 2015

  5. Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)

    2014-09-19

    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

  6. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURES ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    ABSTRACT. Reaction of [VO(acac)2] (acac = acetylacetonate) with ... Single crystal X-ray structural studies indicate that the hydrazone ligands coordinate to ..... Molecular structure of complex (1) at 30% probability displacement. Figure 4.

  7. Theoretical Studies on the Electronic Structures and Properties of Complex Ceramic Crystals and Novel Materials

    Energy Technology Data Exchange (ETDEWEB)

    Ching, Wai-Yim

    2012-01-14

    This project is a continuation of a long program supported by the Office of Basic Energy Science in the Office of Science of DOE for many years. The final three-year continuation started on November 1, 2005 with additional 1 year extension to October 30, 2009. The project was then granted a two-year No Cost Extension which officially ended on October 30, 2011. This report covers the activities within this six year period with emphasis on the work completed within the last 3 years. A total of 44 papers with acknowledgement to this grant were published or submitted. The overall objectives of this project are as follows. These objectives have been evolved over the six year period: (1) To use the state-of-the-art computational methods to investigate the electronic structures of complex ceramics and other novel crystals. (2) To further investigate the defects, surfaces/interfaces and microstructures in complex materials using large scale modeling. (3) To extend the study on ceramic materials to more complex bioceramic crystals. (4) To initiate the study on soft condensed matters including water and biomolecules. (5) To focus on the spectroscopic studies of different materials especially on the ELNES and XANES spectral calculations and their applications related to experimental techniques. (6) To develop and refine computational methods to be effectively executed on DOE supercomputers. (7) To evaluate mechanical properties of different crystals and those containing defects and relate them to the fundamental electronic structures. (8) To promote and publicize the first-principles OLCAO method developed by the PI (under DOE support for many years) for applications to large complex material systems. (9) To train a new generation of graduate students and postdoctoral fellows in modern computational materials science and condensed matter physics. (10) To establish effective international and domestic collaborations with both experimentalists and theorists in materials

  8. Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode.

    Science.gov (United States)

    Bae, Ji-Eun; Kim, In Jung; Nam, Ki Hyun

    2017-11-04

    Glucose isomerase (GI) is an intramolecular oxidoreductase that interconverts aldoses and ketoses. These characteristics are widely used in the food, detergent, and pharmaceutical industries. In order to obtain an efficient GI, identification of novel GI genes and substrate binding/inhibition have been studied. Xylitol is a well-known inhibitor of GI. In Streptomyces rubiginosus, two crystal structures have been reported for GI in complex with xylitol inhibitor. However, a structural comparison showed that xylitol can have variable conformation at the substrate binding site, e.g., a nonspecific binding mode. In this study, we report the crystal structure of S. rubiginosus GI in a complex with xylitol and glycerol. Our crystal structure showed one metal binding mode in GI, which we presumed to represent the inactive form of the GI. The metal ion was found only at the M1 site, which was involved in substrate binding, and was not present at the M2 site, which was involved in catalytic function. The O 2 and O 4 atoms of xylitol molecules contributed to the stable octahedral coordination of the metal in M1. Although there was no metal at the M2 site, no large conformational change was observed for the conserved residues coordinating M2. Our structural analysis showed that the metal at the M2 site was not important when a xylitol inhibitor was bound to the M1 site in GI. Thus, these findings provided important information for elucidation or engineering of GI functions. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Mononuclear mercury(II) complexes containing bipyridine derivatives and thiocyanate ligands: Synthesis, characterization, crystal structure determination, and luminescent properties

    Science.gov (United States)

    Amani, Vahid; Alizadeh, Robabeh; Alavije, Hanieh Soleimani; Heydari, Samira Fadaei; Abafat, Marzieh

    2017-08-01

    A series of mercury(II) complexes, [Hg(Nsbnd N)(SCN)2] (Nsbnd N is 4,4‧-dimethyl-2,2‧-bipyridine in 1, 5,5‧-dimethyl-2,2‧-bipyridine in 2, 6,6‧-dimethyl-2,2‧-bipyridine in 3 and 6-methyl-2,2‧-bipyridine in 4), were prepared from the reactions of Hg(SCN)2 with mentioned ligands in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurement by methanol diffusion into a DMSO solution. The four complexes were thoroughly characterized by spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), elemental analysis (CHNS) and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the mercury(II) cation is four-coordinated in a distorted tetrahedral configuration by two S atoms from two thiocyanate anions and two N atoms from one chelating 2,2‧-bipyridine derivative ligand. Also, in these complexes intermolecular interactions, for example Csbnd H⋯N hydrogen bonds (in 1-4), Csbnd H⋯S hydrogen bonds (in 1, 2 and 4), π … π interactions (in 2-4), Hg⋯N interactions (in 2) and S⋯S interactions (in 4), are effective in the stabilization of the crystal structures and the formation of the 3D supramolecular complexes. Furthermore, the luminescence spectra of the title complexes show that the intensity of their emission bands are stronger than the emission bands for the free bipyridine derivative ligands.

  10. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

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    Reaction of [MoO2(acac)2] (where acac = acetylacetonate) with N'-(2-hydroxy-4- ... Single crystal X-ray structural studies indicate that the hydrazone ligand coordinates .... Molecular structure of the complex at 30% probability displacement.

  11. Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2

    DEFF Research Database (Denmark)

    Broutin, Isabelle; Jomain, Jean-Baptiste; Tallet, Estelle

    2010-01-01

    We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely relate...... and prostate cancer.......We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely related...... PRL receptor (PRLR) ligand. This structure allows one to draw up an exhaustive inventory of the residues involved at the PRL.PRLR site 2 interface, consistent with all previously reported site-directed mutagenesis data. We propose, with this description, an interaction model involving three structural...

  12. Lanthanide complexes with 2,3-dimethoxybenzoic acid and terpyridine. Crystal structures, thermal properties, and antibacterial activities

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Pan-Pan; Wu, Xiao-Hui; Zhang, Jian-Jun [Testing and Analysis Center, Hebei Normal University, Shijiazhuang (China); College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang (China); Ren, Ning [College of Chemical Engineering and Material, Handane College (China); Wang, Shu-Ping [College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang (China)

    2017-08-03

    The lanthanide coordination complexes Er(2,3-DMOBA){sub 3}(terpy)(H{sub 2}O) (1) and [Nd(2,3-DMOBA){sub 3}(terpy)(H{sub 2}O)]{sub 2} (2) (2,3-DMOBA = 2,3-dimethoxybenzoate; terpy = 2,2':6',2{sup ''}-terpyridine) were synthesized and characterized by IR spectroscopy, powder X-ray diffraction (XRD), single-crystal X-ray diffraction, and thermogravimetric analysis. Complex 1 crystallizes in the triclinic system, space group P1, and the mononuclear subunits form a 1D chain structure along the a axis by hydrogen bonds. Complex 2 crystallizes in the monoclinic system, space group P2{sub 1}/c, and the dinuclear subunits are further linked via the offset face-to-face π..π weak stacking interactions to form a supramolecular 2D layered structure. Thermal analysis showed that the complexes have three decomposition steps. The first step is the loss of coordination water molecules. The neutral terpy ligands and partial 2,3-DMOBA ligands are lost in the second step. The remaining 2,3-DMOBA ligands are lost in the third step. The 3D stacked plots for the FT-IR spectra of the evolved gases are recorded and the gaseous products are identified by the typical IR spectra obtained at different temperatures from the 3D stacked plots. Meanwhile, the results of the antibacterial action tests show that 1 and 2 have better antibacterial activities to Candida albicans than to Escherichia coli or Staphylococcus aureus. In addition, complex 2 has better antibacterial action to Candida albicans than complex 1. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Synthesis and X-ray crystal structure of a novel organometallic (µ(3)-oxido)(µ(3)-imido) trinuclear iridium complex

    DEFF Research Database (Denmark)

    Schau-Magnussen, Magnus; Malcho, Phillip; Herbst, Konrad

    2011-01-01

    Reaction of the organometallic aqua ion [Cp*Ir(H(2)O)(3)](2+) with tert-butyl(trimethylsilyl)amine in acetone yielded a novel trinuclear (µ(3)-oxido)(µ(3)-imido)pentamethylcyclopentadienyliridium(iii) complex, [(Cp*Ir)(3)(O)(N(t)Bu)](2+). Single crystal structure analyses show the complex can be ...... that a trinuclear (µ(3)-oxido)(µ(3)-imido) transition metal complex has been structurally characterized....

  14. Synthesis and Crystal Structures of Two Metal Complexes Incorporating Malonate and Organodiamine Ligands

    International Nuclear Information System (INIS)

    Zhang, Quan Zheng; Yang, Wen Bin; Chen, Shu Mei; Lu, Can Zhong

    2005-01-01

    In the present work we report the synthesis and X-ray crystal structures of two new malonato complexes incorporating organodiamine ligands: [Ni(phen)(mal)(H_2O)_2]·3H_2O (H_2mal = malonic acid, phen = 1,10-phenanthroline) and [Zn(bpy)(H_2O)]_2[Zn(bpy)(mal)(H_2O)_2]_2(NO_3)_4·4H_2O (bpy = 2,2'-bipyridine). Investigation on novel organic-inorganic hybrid framework assemblies represents one of the most active areas of material science and chemical research. Major advances have been made in these materials due to their interesting properties and potential in various applications, e. g., electrical conductivity, magnetism, host-guest chemistry, ion exchange, catalysis, nonlinear optics, etc. Moreover, discovery and design of such new materials with specific networks remain of a particularly important and active subject in the field of supramolecuar chemistry and crystal engineering. A variety of complexes with interesting compositions and topologies have been prepared through taking certain factors into account, such as the coordination nature of the metal ion and the shape, functionality, flexibility, and symmetry of organic ligand. Recently, some dicarboxylate ligands, such as oxalate, malonate, and terephthalate, have been widely used in the construction of these interesting structures

  15. Detailed Investigation of the Structural, Thermal, and Electronic Properties of Gold Isocyanide Complexes with Mechano-Triggered Single-Crystal-to-Single-Crystal Phase Transitions.

    Science.gov (United States)

    Seki, Tomohiro; Sakurada, Kenta; Muromoto, Mai; Seki, Shu; Ito, Hajime

    2016-02-01

    Mechano-induced phase transitions in organic crystalline materials, which can alter their properties, have received much attention. However, most mechano-responsive molecular crystals exhibit crystal-to-amorphous phase transitions, and the intermolecular interaction patterns in the daughter phase are difficult to characterize. We have investigated phenyl(phenylisocyanide)gold(I) (1) and phenyl(3,5-dimethylphenylisocyanide)gold(I) (2) complexes, which exhibit a mechano-triggered single-crystal-to-single-crystal phase transition. Previous reports of complexes 1 and 2 have focused on the relationships between the crystalline structures and photoluminescence properties; in this work we have focused on other aspects. The face index measurements of complexes 1 and 2 before and after the mechano-induced phase transitions have indicated that they undergo non-epitaxial phase transitions without a rigorous orientational relationship between the mother and daughter phases. Differential scanning calorimetry analyses revealed the phase transition of complex 1 to be enthalpically driven by the formation of new aurophilic interactions. In contrast, the phase transition of complex 2 was found to be entropically driven, with the closure of an empty void in the mother phase. Scanning electron microscopy observation showed that the degree of the charging effect of both complexes 1 and 2 was changed by the phase transitions, which suggests that the formation of the aurophilic interactions affords more effective conductive pathways. Moreover, flash-photolysis time-resolved microwave conductivity measurements revealed that complex 1 increased in conductivity after the phase change, whereas the conductivity of complex 2 decreased. These contrasting results were explained by the different patterns in the aurophilic interactions. Finally, an intriguing disappearing polymorphism of complex 2 has been reported, in which a polymorph form could not be obtained again after some period of time

  16. Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3

    Directory of Open Access Journals (Sweden)

    Elder John H

    2007-01-01

    Full Text Available Abstract We have obtained the 1.7 Å crystal structure of FIV protease (PR in which 12 critical residues around the active site have been substituted with the structurally equivalent residues of HIV PR (12X FIV PR. The chimeric PR was crystallized in complex with the broad-based inhibitor TL-3, which inhibits wild type FIV and HIV PRs, as well as 12X FIV PR and several drug-resistant HIV mutants 1234. Biochemical analyses have demonstrated that TL-3 inhibits these PRs in the order HIV PR > 12X FIV PR > FIV PR, with Ki values of 1.5 nM, 10 nM, and 41 nM, respectively 234. Comparison of the crystal structures of the TL-3 complexes of 12X FIV and wild-typeFIV PR revealed theformation of additinal van der Waals interactions between the enzyme inhibitor in the mutant PR. The 12X FIV PR retained the hydrogen bonding interactions between residues in the flap regions and active site involving the enzyme and the TL-3 inhibitor in comparison to both FIV PR and HIV PR. However, the flap regions of the 12X FIV PR more closely resemble those of HIV PR, having gained several stabilizing intra-flap interactions not present in wild type FIV PR. These findings offer a structural explanation for the observed inhibitor/substrate binding properties of the chimeric PR.

  17. Magnetic properties and electronic structure of neptunyl(VI) complexes: wavefunctions, orbitals, and crystal-field models

    Energy Technology Data Exchange (ETDEWEB)

    Gendron, Frederic; Pritchard, Ben; Autschbach, Jochen [Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY (United States); Paez-Hernandez, Dayan; Bolvin, Helene [Laboratoire de Physique et de Chimie Quantiques, Universite Toulouse 3 (France); Notter, Francois-Paul [Laboratoire de Chimie Quantique, Universite de Strasbourg (France)

    2014-06-23

    The electronic structure and magnetic properties of neptunyl(VI), NpO{sub 2}{sup 2+}, and two neptunyl complexes, [NpO{sub 2}(NO{sub 3}){sub 3}]{sup -} and [NpO{sub 2}Cl{sub 4}]{sup 2-}, were studied with a combination of theoretical methods: ab initio relativistic wavefunction methods and density functional theory (DFT), as well as crystal-field (CF) models with parameters extracted from the ab initio calculations. Natural orbitals for electron density and spin magnetization from wavefunctions including spin-orbit coupling were employed to analyze the connection between the electronic structure and magnetic properties, and to link the results from CF models to the ab initio data. Free complex ions and systems embedded in a crystal environment were studied. Of prime interest were the electron paramagnetic resonance g-factors and their relation to the complex geometry, ligand coordination, and nature of the nonbonding 5f orbitals. The g-factors were calculated for the ground and excited states. For [NpO{sub 2}Cl{sub 4}]{sup 2-}, a strong influence of the environment of the complex on its magnetic behavior was demonstrated. Kohn-Sham DFT with standard functionals can produce reasonable g-factors as long as the calculation converges to a solution resembling the electronic state of interest. However, this is not always straightforward. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Mechanochemical Synthesis and Crystal Structure of the Lidocaine-Phloroglucinol Hydrate 1:1:1 Complex

    Directory of Open Access Journals (Sweden)

    Nancy Evelyn Magaña-Vergara

    2018-03-01

    Full Text Available Molecular complexation is a strategy used to modify the physicochemical or biopharmaceutical properties of an active pharmaceutical ingredient. Solvent assisted grinding is a common method used to obtain solid complexes in the form of cocrystals. Lidocaine is a drug used as an anesthetic and for the treatment of chronic pain, which bears in its chemical structure an amide functional group able to form hydrogen bonds. Polyphenols are used as cocrystal coformers due to their ability to form O–H···X (X = O, N hydrogen bond interactions. The objective of this study was to exploit the ability of phloroglucinol to form molecular complexes with lidocaine by liquid assisted grinding. The formation of the complex was confirmed by the shift of the O–H and C=O stretching bands in the IR spectra of the polycrystalline ground powders, suggesting the formation of O–H···O=C hydrogen bonds. Hydration of the complexes also was confirmed by IR spectroscopy and by powder X-ray diffraction. The molecular structure was determined by single crystal X-ray diffraction.

  19. Crystal structures of two mononuclear complexes of terbium(III nitrate with the tripodal alcohol 1,1,1-tris(hydroxymethylpropane

    Directory of Open Access Journals (Sweden)

    Thaiane Gregório

    2017-02-01

    Full Text Available Two new mononuclear cationic complexes in which the TbIII ion is bis-chelated by the tripodal alcohol 1,1,1-tris(hydroxymethylpropane (H3LEt, C6H14O3 were prepared from Tb(NO33·5H2O and had their crystal and molecular structures solved by single-crystal X-ray diffraction analysis after data collection at 100 K. Both products were isolated in reasonable yields from the same reaction mixture by using different crystallization conditions. The higher-symmetry complex dinitratobis[1,1,1-tris(hydroxymethylpropane]terbium(III nitrate dimethoxyethane hemisolvate, [Tb(NO32(H3LEt2]NO3·0.5C4H10O2, 1, in which the lanthanide ion is 10-coordinate and adopts an s-bicapped square-antiprismatic coordination geometry, contains two bidentate nitrate ions bound to the metal atom; another nitrate ion functions as a counter-ion and a half-molecule of dimethoxyethane (completed by a crystallographic twofold rotation axis is also present. In product aquanitratobis[1,1,1-tris(hydroxymethylpropane]terbium(III dinitrate, [Tb(NO3(H3LEt2(H2O](NO32, 2, one bidentate nitrate ion and one water molecule are bound to the nine-coordinate terbium(III centre, while two free nitrate ions contribute to charge balance outside the tricapped trigonal-prismatic coordination polyhedron. No free water molecule was found in either of the crystal structures and, only in the case of 1, dimethoxyethane acts as a crystallizing solvent. In both molecular structures, the two tripodal ligands are bent to one side of the coordination sphere, leaving room for the anionic and water ligands. In complex 2, the methyl group of one of the H3LEt ligands is disordered over two alternative orientations. Strong hydrogen bonds, both intra- and intermolecular, are found in the crystal structures due to the number of different donor and acceptor groups present.

  20. Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.

    Science.gov (United States)

    Cardote, Teresa A F; Gadd, Morgan S; Ciulli, Alessio

    2017-06-06

    Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2 VHL complex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  1. Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Lindenberger, Jared J.; Veleti, Sri Kumar; Wilson, Brittney N.; Sucheck, Steven J.; Ronning, Donald R. (Toledo)

    2015-08-06

    GlgE is a bacterial maltosyltransferase that catalyzes the elongation of a cytosolic, branched α-glucan. In Mycobacterium tuberculosis (M. tb), inactivation of GlgE (Mtb GlgE) results in the rapid death of the organism due to a toxic accumulation of the maltosyl donor, maltose-1-phosphate (M1P), suggesting that GlgE is an intriguing target for inhibitor design. In this study, the crystal structures of the Mtb GlgE in a binary complex with maltose and a ternary complex with maltose and a maltosyl-acceptor molecule, maltohexaose, were solved to 3.3 Å and 4.0 Å, respectively. The maltohexaose structure reveals a dominant site for α-glucan binding. To obtain more detailed interactions between first generation, non-covalent inhibitors and GlgE, a variant Streptomyces coelicolor GlgEI (Sco GlgEI-V279S) was made to better emulate the Mtb GlgE M1P binding site. The structure of Sco GlgEI-V279S complexed with α-maltose-C-phosphonate (MCP), a non-hydrolyzable substrate analogue, was solved to 1.9 Å resolution, and the structure of Sco GlgEI-V279S complexed with 2,5-dideoxy-3-O-α-D-glucopyranosyl-2,5-imino-D-mannitol (DDGIM), an oxocarbenium mimic, was solved to 2.5 Å resolution. These structures detail important interactions that contribute to the inhibitory activity of these compounds, and provide information on future designs that may be exploited to improve upon these first generation GlgE inhibitors.

  2. Alignment structures in ferroelectric liquid crystals

    Energy Technology Data Exchange (ETDEWEB)

    Islam, N.U

    1998-07-01

    Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S{sub C} phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes

  3. Alignment structures in ferroelectric liquid crystals

    International Nuclear Information System (INIS)

    Islam, N.U.

    1998-01-01

    Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S C phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes an

  4. Crystal structures of Lymnaea stagnalis AChBP in complex with neonicotinoid insecticides imidacloprid and clothianidin.

    Science.gov (United States)

    Ihara, Makoto; Okajima, Toshihide; Yamashita, Atsuko; Oda, Takuma; Hirata, Koichi; Nishiwaki, Hisashi; Morimoto, Takako; Akamatsu, Miki; Ashikawa, Yuji; Kuroda, Shun'ichi; Mega, Ryosuke; Kuramitsu, Seiki; Sattelle, David B; Matsuda, Kazuhiko

    2008-06-01

    Neonicotinoid insecticides, which act on nicotinic acetylcholine receptors (nAChRs) in a variety of ways, have extremely low mammalian toxicity, yet the molecular basis of such actions is poorly understood. To elucidate the molecular basis for nAChR-neonicotinoid interactions, a surrogate protein, acetylcholine binding protein from Lymnaea stagnalis (Ls-AChBP) was crystallized in complex with neonicotinoid insecticides imidacloprid (IMI) or clothianidin (CTD). The crystal structures suggested that the guanidine moiety of IMI and CTD stacks with Tyr185, while the nitro group of IMI but not of CTD makes a hydrogen bond with Gln55. IMI showed higher binding affinity for Ls-AChBP than that of CTD, consistent with weaker CH-pi interactions in the Ls-AChBP-CTD complex than in the Ls-AChBP-IMI complex and the lack of the nitro group-Gln55 hydrogen bond in CTD. Yet, the NH at position 1 of CTD makes a hydrogen bond with the backbone carbonyl of Trp143, offering an explanation for the diverse actions of neonicotinoids on nAChRs.

  5. Two independent hydrogen bonded complexes of bis(1-piperidiniumacetate) hydrochloride in crystal and in the PM3 optimized structure

    International Nuclear Information System (INIS)

    Dega-Szafran, Z.; Petryna, M.; Dutkiewicz, G.; Kosturkiewicz, Z.

    2003-01-01

    Bis(1-piperidiniumacetate) hydrochloride, (PAA) 2 H · Cl + , has been synthesized and its structure solved by X-ray diffraction. The crystals belong to the triclinic system with two symmetrically independent hydrogen bonded complexes, denoted A and B, at two different inversion centers. The compound crystallizes in the space group P1 with a = 8.559(1), b = 9.625(1), c = 11.441(1) A, α = 74.85(1) o , β = 68.22(1) o , γ 84.10(1) o , Z = 2, R = 0.036. Each complex consists of two 1-piperidiniumacetate moieties. Four 1-piperidiniumacetates, as zwitterions, are held together by a network of hydrogen bonds of the types O...H...O (2.462(3) and 2.463(3) A), N-H...O (2.755(2) A) and N-H...Cl (3.167(2) A). Both N-H atoms in a complex A interact with chlorine anions. A number of weak C-H...Cl contacts stabilize the three-dimensional crystal structure. In the isolated molecule of (PAA) 2 H · Cl + optimized by the PM3 method, there also are two independent hydrogen bonded complexes. In complex A the natural form of 1-piperidineacetic acid interacts with its anionic form, while in complex B the 1-piperidiniumacetic acid, as a cation, forms a hydrogen bond with its zwitterionic form. FTIR spectrum of bis(1-piperidiniumacetate) hydrochloride has been analysed and discussed. (author)

  6. Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor

    International Nuclear Information System (INIS)

    Matsumoto, Yoshiyuki; Kakuda, Shinji; Koizumi, Masahiro; Mizuno, Tsuyoshi; Muroga, Yumiko; Kawamura, Takashi; Takimoto-Kamimura, Midori

    2013-01-01

    The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The present study shows that the benzimidazole ring of the inhibitor takes the stable stacking interaction with the protonated His57 in the catalytic domain of human chymase. The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The X-ray crystallographic study shows that the benzimidazole inhibitor forms a non-covalent interaction with the catalytic domain of human chymase. The hydrophobic fragment of the inhibitor occupies the S1 pocket. The carboxylic acid group of the inhibitor forms hydrogen bonds with the imidazole N(∊) atom of His57 and/or the O(γ) atom of Ser195 which are members of the catalytic triad. This imidazole ring of His57 induces π–π stacking to the benzene ring of the benzimidazole scaffold as P2 moiety. Fragment molecular orbital calculation of the atomic coordinates by X-ray crystallography shows that this imidazole ring of His57 could be protonated with the carboxyl group of Asp102 or hydroxyl group of Ser195 and the stacking interaction is stabilized. A new drug design strategy is proposed where the stacking to the protonated imidazole of the drug target protein with the benzimidazole scaffold inhibitor causes unpredicted potent inhibitory activity for some enzymes

  7. Synthesis and crystal structure of a polymeric zinc(II complex derived from 4-nitro- phenylacetic acid and propane-1,3-diamine

    Directory of Open Access Journals (Sweden)

    G-H. Sheng

    2014-05-01

    Full Text Available A new polymeric zinc(II complex, [ZnL2(PDA]n, has been prepared by the reaction of zinc sulfate, 4-nitrophenylacetic acid, and propane-1,3-diamine (PDA in water. Structure of the complex has been characterized by single-crystal X-ray diffraction. The complex crystallizes as orthorhombic space group Pnma, with unit cell dimensions a = 15.732(1 Å, b = 23.912(1 Å, c = 5.5565(3 Å, V = 2090.2(2 Å3, Z = 4, R1 = 0.0427, wR2 = 0.0968, S = 1.048. The Zn atom is coordinated in a tetrahedral geometry. Single crystals of the complex are stabilized by hydrogen bonds and p···p interactions. DOI: http://dx.doi.org/10.4314/bcse.v28i2.17

  8. Syntheses, Crystal Structures and Thermal Behaviors of Two Supramolecular Salamo-Type Cobalt(II and Zinc(II Complexes

    Directory of Open Access Journals (Sweden)

    Gang Li

    2017-07-01

    Full Text Available This paper reports the syntheses of two new complexes, [Co(L1(H2O2] (1 and [{Zn(L2(μ-OAcZn(n-PrOH}2] (2, from asymmetric halogen-substituted Salamo-type ligands H2L1 and H3L2, respectively. Investigation of the crystal structure of complex 1 reveals that the complex includes one Co(II ion, one (L12− unit and two coordinated water molecules. Complex 1 shows slightly distorted octahedral coordination geometry, forming an infinite 2D supramolecular structure by intermolecular hydrogen bond and π–π stacking interactions. Complex 2 contains four Zn(IIions, two completely deprotonated (L23− moieties, two coordinated μ-OAc− ions and n-propanol molecules. The Zn(II ions in complex 2 display slightly distorted trigonal bipyramidal or square pyramidal geometries.

  9. Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars.

    Science.gov (United States)

    Chan, Hsiu-Chien; Zhu, Yueming; Hu, Yumei; Ko, Tzu-Ping; Huang, Chun-Hsiang; Ren, Feifei; Chen, Chun-Chi; Ma, Yanhe; Guo, Rey-Ting; Sun, Yuanxia

    2012-02-01

    D-psicose 3-epimerase (DPEase) is demonstrated to be useful in the bioproduction of D-psicose, a rare hexose sugar, from D-fructose, found plenty in nature. Clostridium cellulolyticum H10 has recently been identified as a DPEase that can epimerize D-fructose to yield D-psicose with a much higher conversion rate when compared with the conventionally used DTEase. In this study, the crystal structure of the C. cellulolyticum DPEase was determined. The enzyme assembles into a tetramer and each subunit shows a (β/α)(8) TIM barrel fold with a Mn(2+) metal ion in the active site. Additional crystal structures of the enzyme in complex with substrates/products (D-psicose, D-fructose, D-tagatose and D-sorbose) were also determined. From the complex structures of C. cellulolyticum DPEase with D-psicose and D-fructose, the enzyme has much more interactions with D-psicose than D-fructose by forming more hydrogen bonds between the substrate and the active site residues. Accordingly, based on these ketohexose-bound complex structures, a C3-O3 proton-exchange mechanism for the conversion between D-psicose and D-fructose is proposed here. These results provide a clear idea for the deprotonation/protonation roles of E150 and E244 in catalysis.

  10. Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

    KAUST Repository

    Dumbrack, Roland

    2016-01-01

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine

  11. Complexation of 1,3-dimorpholinopropane with Hg(II) and Zn(II) salts: Synthese, crystal structures and antibacterial studies

    Czech Academy of Sciences Publication Activity Database

    Goudarziafshar, H.; Yousefi, S.; Abbasityula, Y.; Dušek, Michal; Eigner, Václav; Rezaeivala, M.; Özbek, N.

    2015-01-01

    Roč. 31, č. 6 (2015), s. 1076-1084 ISSN 1001-4861 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : crystal structure * 1,3-dimorpholinopropane * antibacterial activity * Hg(II) complex * Zn(II) complex Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 0.488, year: 2015

  12. Goos-Haenchen shift in complex crystals

    Energy Technology Data Exchange (ETDEWEB)

    Longhi, Stefano; Della Valle, Giuseppe; Staliunas, Kestutis [Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Departament de Fisica i Enginyeria Nuclear, Instituci Catalana de Recerca i Estudis Avanats (ICREA), Universitat Politcnica de Catalunya, Colom 11, E-08222 Terrassa, Barcelona (Spain)

    2011-10-15

    The Goos-Haenchen (GH) effect for wave scattering from complex PT-symmetric periodic potentials (complex crystals) is theoretically investigated, with specific reference to optical GH shift in photonic crystal slabs with a sinusoidal periodic modulation of both real and imaginary parts of the dielectric constant. The analysis highlights some distinct and rather unique features as compared to the GH shift found in ordinary crystals. In particular, as opposed to GH shift in ordinary crystals, which is large at the band gap edges, in complex crystals the GH shift can be large inside the reflection (amplification) band and becomes extremely large as the PT symmetry-breaking threshold is approached.

  13. Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    International Nuclear Information System (INIS)

    Filippova, E. V.; Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-01-01

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI 2 with the coupled reduction of nicotinamide adenine dinucleotide (NAD + ). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD + -azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state

  14. Crystal and macular structure of 1:1 complex of N-methylmorpholine betaine with salicylic acid

    International Nuclear Information System (INIS)

    Bartoszak-Adamska, E.; Dega-Szafran, Z.; Przedwojska, M.; Jaskolski, M.

    2003-01-01

    The structure of a 1:1 complexes of complex of N-methylmorpholine betaine (MMB) with salicylic acid (SAL) has been determined by a single crystal X-ray analysis. The crystals are orthorhombic, space group Pbca, with a 9.4702(6), b = 13.0559(7) and c = 45.226(2) A (at 140 K). The asymmetric unit is composed of two MMB + ·SAL - units (A and B) each formed by a short, nearly linear O-H...O hydrogen bond (2.542(2) and 2.474(2) A) between the carboxylic group of the betaine cation and carboxylate group of the anion. The salicylate anions form short intramolecular O-H...O hydrogen bonds of 2. 472(2) and 2.525(2) A (O-H...O angles 160(2) and 149(2) o ) for anion A and B, respectively, between the ortho hydroxyl donor and the COO - group, but the carboxylate acceptor O atom is in each case different. The morpholine rings are in a chair conformation with the -CH 2 COOH group in equatorial and the methyl group in axial positions. FTIR, and 1 H and 13 C NMR spectra of the complex are discussed. (author)

  15. Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly

    Science.gov (United States)

    Cottee, Matthew A; Muschalik, Nadine; Wong, Yao Liang; Johnson, Christopher M; Johnson, Steven; Andreeva, Antonina; Oegema, Karen; Lea, Susan M; Raff, Jordan W; van Breugel, Mark

    2013-01-01

    Centrioles organise centrosomes and template cilia and flagella. Several centriole and centrosome proteins have been linked to microcephaly (MCPH), a neuro-developmental disease associated with small brain size. CPAP (MCPH6) and STIL (MCPH7) are required for centriole assembly, but it is unclear how mutations in them lead to microcephaly. We show that the TCP domain of CPAP constitutes a novel proline recognition domain that forms a 1:1 complex with a short, highly conserved target motif in STIL. Crystal structures of this complex reveal an unusual, all-β structure adopted by the TCP domain and explain how a microcephaly mutation in CPAP compromises complex formation. Through point mutations, we demonstrate that complex formation is essential for centriole duplication in vivo. Our studies provide the first structural insight into how the malfunction of centriole proteins results in human disease and also reveal that the CPAP–STIL interaction constitutes a conserved key step in centriole biogenesis. DOI: http://dx.doi.org/10.7554/eLife.01071.001 PMID:24052813

  16. Crystallization of Mitochondrial Respiratory Complex II fromChicken Heart: A Membrane-Protein Complex Diffracting to 2.0Angstrom

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward A.

    2004-12-17

    Procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Angstrom with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites.

  17. New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

    Science.gov (United States)

    Tabti, Salima; Djedouani, Amel; Aggoun, Djouhra; Warad, Ismail; Rahmouni, Samra; Romdhane, Samir; Fouzi, Hosni

    2018-03-01

    The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

  18. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function

    DEFF Research Database (Denmark)

    Rowland, Paul; Bjørnberg, Olof; Nielsen, Finn S.

    1998-01-01

    Dihydroorotate dehydrogenases (DHODs) catalyze the oxidation of (S)-dihydroorotate to orotate, the fourth step and only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. A description is given of the crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A (DHODA......) complexed with the product of the enzyme reaction orotate. The structure of the complex to 2.0 A resolution has been compared with the structure of the native enzyme. The active site of DHODA is known to contain a water filled cavity buried beneath a highly conserved and flexible loop. In the complex...

  19. Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG).

    Science.gov (United States)

    Saminadin, P; Dautant, A; Mondon, M; Langlois D'estaintot, B; Courseille, C; Précigoux, G

    2000-01-01

    Doxorubicin is among the most widely used anthracycline in cancer chemotherapy. In an attempt to avoid the cardiotoxicity and drug resistance of doxorubicin therapy, several analogues were synthesized. The cyanomorpholinyl derivative is the most cytotoxic. They differ greatly from their parent compound in their biological and pharmacological properties, inducing cross-links in drug DNA complexes. The present study concerns N-cyanomethyl-N-(2-methoxyethyl)-daunomycin (CMDa), a synthetic analogue of cyanomorpholino-daunomycin. Compared to doxorubicin, CMDa displays a cytotoxic activity on L1210 leukemia cells at higher concentration but is effective on doxorubicin resistant cells. The results of fluorescence quenching experiments as well as the melting temperature (DeltaTm = 7.5 degrees C) studies are consistent with a drug molecule which intercalates between the DNA base pairs and stabilizes the DNA double helix. The crystal structure of CMDa complexed to the hexanucleotide d(CGATCG) has been determined at 1.5 A resolution. The complex crystallizes in the space group P41212 and is similar to other anthracycline-hexanucleotide complexes. In the crystal state, the observed densities indicate the formation of N-hydroxymethyl-N-(2-methoxyethyl)-daunomycin (HMDa) with the release of the cyano moiety without DNA alkylation. The formation of this degradation compound is discussed in relation with other drug modifications when binding to DNA. Comparison with two other drug-DNA crystal structures suggests a correlation between a slight change in DNA conformation and the nature of the amino sugar substituents at the N3' position located in the minor groove.

  20. Synthesis, characterization and crystal structure of a ...

    African Journals Online (AJOL)

    The Mo atom in the complex is in octahedral coordination. Thermal stability of the complex has also been studied. KEY WORDS: Molybdenum complex, Hydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. Bull. Chem. Soc. Ethiop. 2014, 28(3), 409-414. DOI: http://dx.doi.org/10.4314/bcse.v28i3.10 ...

  1. Synthesis, crystal and band structures, and properties of a new supramolecular complex (Hg2As)2(CdI4)

    International Nuclear Information System (INIS)

    Zou Jianping; Wu Dongsheng; Huang Shuping; Zhu Jing; Guo Guocong; Huang Jinshun

    2007-01-01

    A new quaternary supramolecular complex (Hg 2 As) 2 (CdI 4 ) (1) has been prepared by the solid-state reaction and structurally characterized by single crystal X-ray diffraction analysis. Compound 1 crystallizes in the space group P2 1 of the monoclinic system with two formula units in a cell: a=7.945(4), b=12.934(6), c=8.094(4) A, β=116.898 o (1), V=741.7(6) A 3 . The structure of 1 is characterized by a tridymite-like three-dimensional cationic framework, which is composed of mercury and arsenic atoms, with the channels being occupied by discrete CdI 4 2- tetrahedral guest-anions. The optical properties were investigated in terms of the diffuse reflectance and Fourier transform infrared spectra. The electronic band structure along with density of states (DOS) calculated by DFT method indicates that the present compound is a semiconductor with a direct band gap, and that the optical absorption is mainly originated from the charge transitions from I-5p and As-4p to Cd-5s and Hg-6s states. - Graphical abstract: A new quaternary supramolecular complex (Hg 2 As) 2 (CdI 4 ) (1) has been prepared by the solid-state reaction, and structurally characterized by single crystal X-ray diffraction analysis. The structure of 1 is characterized by a 3-D tridymite-like cationic framework with the channels being occupied by discrete CdI 4 2- tetrahedral guest-anions

  2. Synthesis and crystal structure of a homoleptic diruthenium complex containing tetra-2-pyridyl-1,4-pyrazine (tppz)

    Energy Technology Data Exchange (ETDEWEB)

    Graf, Marion; Mayer, Peter; Boettcher, Hans-Christian [Muenchen Univ. (Germany). Dept. Chemie

    2017-07-01

    Treatment of hydrated ruthenium(III) chloride with tetra-2-pyridyl-1,4-pyrazine (tppz) in refluxing ethoxyethanol afforded the homoleptic dinuclear complex [(tppz)Ru(μ-tppz)Ru(tppz)]{sup 4+} (1) besides small amounts of the species [Ru(tppz){sub 2}]{sup 2+}. The title complex 1 was obtained as purple crystals and characterized as its hexafluoridophosphate salt by NMR spectroscopy, mass spectrometry and microanalyses. The molecular structure of 1(PF{sub 6}){sub 4} has been established by X-ray crystallography.

  3. High-resolution crystal structure of Streptococcus pyogenes β-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    International Nuclear Information System (INIS)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

    2013-01-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD + glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD + glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN ct –IFS complex, which consists of the SPN C-terminal domain (SPN ct ; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN ct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope

  4. The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4.

    Science.gov (United States)

    Isabet, Tatiana; Montagnac, Guillaume; Regazzoni, Karine; Raynal, Bertrand; El Khadali, Fatima; England, Patrick; Franco, Michel; Chavrier, Philippe; Houdusse, Anne; Ménétrey, Julie

    2009-09-16

    The JNK-interacting proteins, JIP3 and JIP4, are specific effectors of the small GTP-binding protein ARF6. The interaction of ARF6-GTP with the second leucine zipper (LZII) domains of JIP3/JIP4 regulates the binding of JIPs to kinesin-1 and dynactin. Here, we report the crystal structure of ARF6-GTP bound to the JIP4-LZII at 1.9 A resolution. The complex is a heterotetramer with dyad symmetry arranged in an ARF6-(JIP4)(2)-ARF6 configuration. Comparison of the ARF6-JIP4 interface with the equivalent region of ARF1 shows the structural basis of JIP4's specificity for ARF6. Using site-directed mutagenesis and surface plasmon resonance, we further show that non-conserved residues at the switch region borders are the key structural determinants of JIP4 specificity. A structure-derived model of the association of the ARF6-JIP3/JIP4 complex with membranes shows that the JIP4-LZII coiled-coil should lie along the membrane to prevent steric hindrances, resulting in only one ARF6 molecule bound. Such a heterotrimeric complex gives insights to better understand the ARF6-mediated motor switch regulatory function.

  5. Crystal structure of the β2 adrenergic receptor-Gs protein complex

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, Søren G.F.; DeVree, Brian T; Zou, Yaozhong; Kruse, Andrew C; Chung, Ka Young; Kobilka, Tong Sun; Thian, Foon Sun; Chae, Pil Seok; Pardon, Els; Calinski, Diane; Mathiesen, Jesper M; Shah, Syed T.A.; Lyons, Joseph A; Caffrey, Martin; Gellman, Samuel H; Steyaert, Jan; Skiniotis, Georgios; Weis, William I; Sunahara, Roger K; Kobilka, Brian K [Brussels; (Trinity); (Michigan); (Stanford-MED); (Michigan-Med); (UW)

    2011-12-07

    G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein) by an agonist-occupied receptor. The β2 adrenergic receptor (β2AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β2AR and nucleotide-free Gs heterotrimer. The principal interactions between the β2AR and Gs involve the amino- and carboxy-terminal α-helices of Gs, with conformational changes propagating to the nucleotide-binding pocket. The largest conformational changes in the β2AR include a 14Å outward movement at the cytoplasmic end of transmembrane segment 6 (TM6) and an α-helical extension of the cytoplasmic end of TM5. The most surprising observation is a major displacement of the α-helical domain of Gαs relative to the Ras-like GTPase domain. This crystal structure represents the first high-resolution view of transmembrane signalling by a GPCR.

  6. Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions.

    Science.gov (United States)

    Chandrasekhar, Sosale; Naik, Tangali R Ravikumar; Nayak, Susanta K; Row, Tayur N Guru

    2010-06-15

    The titled complex, obtained by co-crystallization (EtOH/25 degrees C), is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. Copyright 2010 Elsevier Ltd. All rights reserved.

  7. Synthesis, crystal structure and bioactivity of manganese complexes with asymmetric chiral Schiff base

    Science.gov (United States)

    Zhang, Enfeng; Wei, Yi; Huang, Fuping; Yu, Qing; Bian, Hedong; Liang, Hong; Lei, Fuhou

    2018-03-01

    A couple of chiral unsymmtrical Schiff base ligands, (1R,2R) (-)chxn (salH) (naftalH) and (1S,2S) (-)chxn (salH) (naftalH) had been synthesized by the condensation of salicylaldehyde and 2-hydroxy-1-naphthaldehyde with two isomers of (1R,2R)-trans-1,2-cyclohexanediamin and (1S,2S)-trans-1,2-cyclohexanediamin, respectively. At the same time, two manganese complexes have been synthesized and fully characterized by FT-IR spectrum, elemental analyses, single crystal X-ray diffraction. The interaction of the two Mn (III) complexes with bovine serum albumin (BSA) was investigated by spectroscopic techniques. The result reveals that the complexes can strongly quench the intrinsic fluorescence of BSA through a static quenching mechanism. The binding constant and binding mode has been determined. The secondary structure and the amino acid residues microenvironment of BSA change in the presence of these complexes. SOD-like activity and ABTS free radical scavenging ability were also studied. The antioxidant capacity of the compounds showed that the complexes and their corresponding BSA adducts showed some SOD activity. The results of ABTS free radical scavenging showed that the activity of the BSA adduct was more obvious than that of the complex.

  8. Synthesis, characterization and x-ray crystal structure of a dimethyltin (IV) dichloride complex of 2-acetylpyridine benzophenone azine

    International Nuclear Information System (INIS)

    Mustaffa Shamsuddin; Md Abu Affan; Ramli Atan

    1998-01-01

    Dimethyltin dichloride react with 2-ac ethylpyridine benzophenone azine (apba) in refluxing dry hexane to give (SnMe 2 Cl 2 (apba)) where the azine ligand acts as a bidentate N-N chelating ligand. The complex has been characterized by IR spectroscopy, 1 H and 13 C NMR spectroscopic data and elemental analyses. The crystal structure of the dimethyltin(IV) derivative has also been determined. Crystals are monoclinic with space group P2(1)/n with cell dimensions: a = 10.1819(3) Armstrong, b = 18.3113(5) Armstrong, c = 12.6451(4) Armstrong

  9. Complex assembly, crystallization and preliminary X-ray crystallographic studies of rhesus macaque MHC Mamu-A*01 complexed with an immunodominant SIV-Gag nonapeptide

    International Nuclear Information System (INIS)

    Chu, Fuliang; Lou, Zhiyong; Gao, Bin; Bell, John I.; Rao, Zihe; Gao, George F.

    2005-01-01

    Crystallization of the first rhesus macaque MHC class I complex. Simian immunodeficiency virus (SIV) infection in rhesus macaques has been used as the best model for the study of human immunodeficiency virus (HIV) infection in humans, especially in the cytotoxic T-lymphocyte (CTL) response. However, the structure of rhesus macaque (or any other monkey model) major histocompatibility complex class I (MHC I) presenting a specific peptide (the ligand for CTL) has not yet been elucidated. Here, using in vitro refolding, the preparation of the complex of the rhesus macaque MHC I allele (Mamu-A*01) with human β 2 m and an immunodominant peptide, CTPYDINQM (Gag-CM9), derived from SIV Gag protein is reported. The complex (45 kDa) was crystallized; the crystal belongs to space group I422, with unit-cell parameters a = b = 183.8, c = 155.2 Å. The crystal contains two molecules in the asymmetric unit and diffracts X-rays to 2.8 Å resolution. The structure is being solved by molecular replacement and this is the first attempt to determined the crystal structure of a peptide–nonhuman primate MHC complex

  10. Preparation of three terbium complexes with p-aminobenzoic acid and investigation of crystal structure influence on luminescence property

    International Nuclear Information System (INIS)

    Ye Chaohong; Sun Haoling; Wang Xinyi; Li Junran; Nie Daobo; Fu Wenfu; Gao Song

    2004-01-01

    Three new rare earth p-aminobenzoic acid complexes, [Tb 2 L 6 (H 2 O) 2 ] n (1), [Tb 2 L 6 (H 2 O) 4 ].2H 2 O (2) and [Tb(phen) 2 L 2 (H 2 O) 2 ](phen)L·4H 2 O (3) (HL: p-aminobenzoic acid; phen: 1, 10-phenanthroline), with different structural forms are reported in this paper. Complex 1 is a polymolecule with a two-dimensional plane structure. Compound 2 is a binuclear molecule, and 3 appears to be a mononuclear complex. The fluorescence intensity, the fluorescence life-time and emission quantum yield of 2, which has two coordination water molecules, is better than those of 1, which has only one coordination water molecule. This is an unusual phenomenon for general fluorescent rare earth complexes. The fluorescence performance of 3 is the most unsatisfactory among the three complexes. Their crystal structures show that the coordination mode of the ligand is an important factor influencing the luminescence properties of a fluorescent rare earth complex

  11. Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes.

    Science.gov (United States)

    Kim, H; Lipscomb, W N

    1990-06-12

    O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity (Ki = 3 pM). Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis [Hanson, J. E., Kaplan, A. P., & Bartlett, P. A. (1989) Biochemistry 28, 6294-6305]. In the present study, the structure of the complex of this phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 A. The complex crystallizes in the space group P2(1)2(1)2(1) with cell dimensions a = 61.9 A, b = 67.2 A, and c = 76.2 A. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 A yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 A on the electrophilic (Arg-127) side and 3.1 A on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attacked by Zn-hydroxyl (or Zn-water). An unexpected feature of the bound inhibitor, the cis carbamoyl ester bond at the benzyloxycarbonyl linkage to alanine, allows the benzyloxycarbonyl phenyl ring of the inhibitor to interact favorably with Tyr-198. This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.

  12. Determination of crystal structures by x-ray diffraction: applications to a lanthanide complex and a natural organic compound

    International Nuclear Information System (INIS)

    Miranda, J.M. de.

    1986-01-01

    The study fir determining crystal structures of the Ho (ReO sub(4)) sub(3) 4 TDTD 3 H sub(2) O complex and the natural organic compound C sub(14) H sub(16) O sub(6) by X-ray diffraction are presented. The experimental equipments are described in details. (M.C.K.)

  13. short communication synthesis and crystal structure of a polymeric

    African Journals Online (AJOL)

    Preferred Customer

    A new polymeric zinc(II) complex, [ZnL2(PDA)]n, has been prepared by the reaction of zinc sulfate ... complex has been characterized by single-crystal X-ray diffraction. .... Molecular structure of the complex at 30% probability displacement.

  14. Remedial Strategies in Structural Proteomics: Expression, Purification, And Crystallization of the Vav1/Rac1 Complex

    Energy Technology Data Exchange (ETDEWEB)

    Brooun, A.; Foster, S.A.; Chrencik, H.E.; Chien, E.Y.T.; Kolatkar, A.R.; Streiff, M.; Ramage, P.; Widmer, H.; Weckbecker, G.; Kuhn, P.

    2007-07-03

    The signal transduction pathway involving the Vav1 guanine nucleotide exchange factor (GEF) and the Rac1 GTPase plays several key roles in the immune response mediated by the T cell receptor. Vav1 is also a unique member of the GEF family in that it contains a cysteine-rich domain (CRD) that is critical for Rac1 binding and maximal guanine nucleotide exchange activity, and thus may provide a unique protein-protein interface compared to other GEF/GTPase pairs. Here, we have applied a number of remedial structural proteomics strategies, such as construct and expression optimization, surface mutagenesis, limited proteolysis, and protein formulation to successfully express, purify, and crystallize the Vav1-DH-PH-CRD/Rac1 complex in an active conformation. We have also systematically characterized various Vav1 domains in a GEF assay and Rac1 in vitro binding experiments. In the context of Vav1-DH-PH-CRD, the zinc finger motif of the CRD is required for the expression of stable Vav1, as well as for activity in both a GEF assay and in vitro formation of a Vav1/Rac1 complex suitable for biophysical and structural characterization. Our data also indicate that the isolated CRD maintains a low level of specific binding to Rac1, appears to be folded based on 1D NMR analysis and coordinates two zinc ions based on ICP-MS analysis. The protein reagents generated here are essential tools for the determination of a three dimensional Vav1/Rac1 complex crystal structure and possibly for the identification of inhibitors of the Vav1/Rac1 protein-protein interaction with potential to inhibit lymphocyte activation.

  15. Iron(II) tris(3-bromo-1,10-phenanthroline) complex:synthesis, crystal structure and electropolymerization

    CERN Document Server

    Lee, K J; Lee, S S; Lee, B Y

    2002-01-01

    The complex of iron(II) tris(3-Br-phen)(3-Br-phen; 3-bromo-1,10-phenanthroline) was prepared as a precursor of electropolymerization and the crystal structure of [Fe(3-Br-phen) sub 3](PF sub 6) sub 2 centre dot CH sub 3 CN with a distorted octahedral geometry has been investigated. The reductive electropolymerization of [Fe(3-Br-phen) sub 3] sup 2 sup + complex onto the surface of a glassy carbon electrode and indium tin oxide (ITO) optically transparent electrode were performed in acetonitrile at room temperature. Thin film of poly-[Fe(3-Br-phen) sub 3] sup 2 sup + formed was adherent, electroactive and stably deposited on a glassy carbon disk electrode. The thin metallopolymeric film formed was also confirmed by absorption spectroscopy.

  16. Complex assembly, crystallization and preliminary X-ray crystallographic studies of duck MHC class I molecule

    International Nuclear Information System (INIS)

    Zhang, Jianhua; Chen, Yong; Gao, Feng; Chen, Weihong; Qi, Jianxun; Xia, Chun

    2009-01-01

    Using a peptide derived from H5N1, a complex of duck MHC class I molecule (DuMHC I) with duck β 2 -microglobulin (Duβ 2 m) was assembled and crystallized. Initial structure analysis indicated that the crystals did not contain the complete DuMHC I complex but instead contained DuMHC I α3-domain and Duβ 2 m subunits. In order to understand the biological properties of the immune systems of waterfowl and to establish a system for structural studies of duck class I major histocompatibility complex (DuMHC I), a complex of DuMHC I with duck β 2 -microglobulin (Duβ 2 m) and the peptide AEIEDLIF (AF8) derived from H5N1 NP residues 251–258 was assembled. The complex was crystallized; the crystals belonged to space group C222 1 , with unit-cell parameters a = 54.7, b = 72.4, c = 102.2 Å, and diffracted to 2.3 Å resolution. Matthews coefficient calculation and initial structure determination by molecular replacement showed that the crystals did not contain the whole DuMHC I complex, but instead contained the DuMHC I α3 domain and a Duβ2m molecule (DuMHC I α3+β2m). Another complex of DuMHC I with the peptide IDWFDGKE derived from a chicken fusion protein also generated the same results. The stable structure of DuMHC I α3+β2m may reflect some unique characteristics of DuMHC I and pave the way for novel MHC structure-related studies in the future

  17. Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of Co(II)- picolinate complex

    Energy Technology Data Exchange (ETDEWEB)

    Tamer, Ömer, E-mail: omertamer@sakarya.edu.tr; Avcı, Davut; Atalay, Yusuf

    2015-11-15

    A cobalt(II) complex of picolinate was synthesized, and its structure was fully characterized by the applying of X-ray diffraction method as well as FT-IR, FT-Raman and UV–vis spectroscopies. In order to both support the experimental results and convert study to more advanced level, density functional theory calculations were performed by using B3LYP level. Single crystal X-ray structural analysis shows that cobalt(II) ion was located to the center of distorted octahedral geometry. The C=O, C=C and C=N stretching vibrations were found as highly active and strong peaks, inducing the molecular charge transfer within Co(II) complex. The small energy gap between frontier molecular orbital energies was another indicator of molecular charge transfer interactions within Co(II) complex. The nonlinear optical properties of Co(II) complex were investigated at DFT/B3LYP level, and the hypepolarizability parameter was found to be decreased due to the presence of inversion symmetry. The natural bond orbital (NBO) analysis was performed to investigate molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength for Co(II) complex. Finally, molecular electrostatic potential (MEP) and spin density distributions for Co(II) complex were evaluated. - Highlights: • Co(II) complex of picolinate was prepared. • Its FT-IR, FT-Raman and UV–vis spectra were measured. • DFT calculations were performed to support experimental results. • Small HOMO-LUMO energy gap is an indicator of molecular charge transfer. • Spin density localized on Co(II) as well as O and N atoms.

  18. Three phenoxo-bridged dinuclear lanthanide complexes. Syntheses, crystal structures, and magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhi-Chao; Dai, Rui-Peng; Yang, En-Cui [College of Chemistry, Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, Tianjin Normal University (China); Dong, Hui-Ming; Zhao, Xiao-Jun [College of Chemistry, Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, Tianjin Normal University (China); Department of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin (China)

    2018-03-15

    Three dinuclear lanthanide complexes [Ln{sub 2}(H{sub 2}L){sub 2}(NO{sub 3}){sub 4}] [Ln = Dy (1), Tb (2), and Gd (3)] [H{sub 3}L = 2-hydroxyimino-N'-[(2-hydroxy-3-methoxyphenyl)methylidene]- propanohydrazone] were solvothermally synthesized by varying differently anisotropic rare earth ions. Single-crystal structural analyses demonstrate that all the three complexes are crystallographically isostructural with two centrosymmetric Ln{sup III} ions aggregated by a pair of monodeprotonated H{sub 2}L{sup -} anions. Weak intramolecular antiferromagnetic interactions with different strength were mediated by a pair of phenoxo bridges due to superexchange and/or single-ion anisotropy. Additionally, the Dy{sup III}-based entity shows the strongest anisotropy exhibits field-induced single-molecule magnetic behavior with two thermally activated relaxation processes. In contrast, 3 with isotropic Gd{sup III} ion has a significant cryogenic magnetocaloric effect with the maximum entropy change of 25.7 J.kg{sup -1}.K{sup -1} at 2.0 K and 70.0 kOe. (copyright 2018 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jiansheng; Natarajan, Kannan; Boyd, Lisa F.; Morozov, Giora I.; Mage, Michael G.; Margulies, David H. (NIH); (Hebrew)

    2017-10-12

    Central to CD8+ T cell–mediated immunity is the recognition of peptide–major histocompatibility complex class I (p–MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein–related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.

  20. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    Science.gov (United States)

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions.

  1. Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.

    Science.gov (United States)

    Numata, Tomoyuki; Inanaga, Hideko; Sato, Chikara; Osawa, Takuo

    2015-01-30

    Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3-Csm4 subcomplex at 3.1Å resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1-Csm4-Csm3 ternary complex, which provides insights into its role in the Csm interference complex. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Crystal structures of LiCsTiF6 and Cs2TiF6 and interval mobility of complex anions

    International Nuclear Information System (INIS)

    Popov, D.Yu.; Kavun, V.Ya.; Gerasimenko, A.V.; Sergienko, V.I.; Antokhina, T.F.

    2002-01-01

    The structure of LiCsTiF 6 (1) and Cs 2 TiF 6 (2) monocrystals was studied by the method of X-ray diffraction analysis. Crystal lattice parameters for compound 1 are: a = 9.251 (1), b = 11.920 (1), c = 10.271 (1), sp.gr. Pbcn, Z = 8; for compound 2: a = 6.213 (1), c = 5.004 (1), sp.gr. P3-bar m1, Z = 1. Three-dimensional frame of bound titanium octahedrons and slightly distorted lithium tetragonal pyramids with Li-F distance ranging from 1.86 to 2.24 A is the crystal structure base of compound 1. The structure of compound 2 is made of dose-packed CsF 3 layers and TiF 6 2- octahedrons located between the layers. The types of internal motion of the complex anions were determined by 10 F NMR method, their activation energy in crystals 1 and 2 in the temperature range of 200-500 K being estimated [ru

  3. Chromium(III) Complex Obtained from Dipicolinic Acid: Synthesis, Characterization, X-Ray Crystal Structure and Electrochemical Studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghasemi, Khaled; Rezvani, Ali Reza; Ghasemi, Fatemeh [Univ. of Sistan and Baluchestan, Zahedan (Iran, Islamic Republic of); Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim [Universiti Sains Malaysia, Penang (Malaysia)

    2013-10-15

    The synthesis, X-ray crystallography, spectroscopic (IR, UV-vis), and electrochemical properties of the title compound, [H{sub 3}O][Cr(dipic){sub 2}] [H{sub 3}O{sup +}.Cl{sup -}] (1), (H{sub 2}dipic = 2,6-pyridinedicarboxylic acid), are reported. This complex crystallizes in the monoclinic space group Cc with a = 14.9006(10) A, b = 12.2114(8) A, c = 8.6337(6) A, α = 90.00 .deg., β = 92.7460(10) .deg., γ = 90.00 .deg., and V = 1569.16(18) A3 with Z = 4. The hydrogen bonding and noncovalent interactions play roles in the stabilization of the structure. In order to gain a better understanding of the most important geometrical parameters in the structure of the complex, atoms in molecules (AIM) method at B3LYP/6-31G level of theory has been employed.

  4. Crystal structure of the conserved herpesvirus fusion regulator complex gH—gL

    Energy Technology Data Exchange (ETDEWEB)

    Chowdary, Tirumala K.; Cairns, Tina M.; Atanasiu, Doina; Cohen, Gary H.; Eisenberg, Roselyn J.; Heldwein, Ekaterina E. [UPENN; (Tufts-MED)

    2015-02-09

    Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH–gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH–gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, we propose that gH–gL activates gB for fusion, possibly through direct binding. Formation of a gB–gH–gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB–gH–gL interface a promising antiviral target.

  5. Crystal structures of titanium–aluminium and –gallium complexes bearing two μ2-CH3 units

    Directory of Open Access Journals (Sweden)

    Tim Oswald

    2017-05-01

    Full Text Available The isotypic crystal structures of two titanocene complexes containing an EMe3 unit (E = Al, Ga; Me = methyl with two μ2-coordinating methyl groups, namely [μ-1(η5-(adamantan-1-yl-2κC1cycylopentadienyl]di-μ2-methyl-methyl-2κC-[1(η5-pentamethylcyclopentadienyl]aluminiumtitanium(III, [AlTi(CH33(C10H15(C15H18], and [μ-1(η5-(adamantan-1-yl-2κC1cycylopentadienyl]di-μ2-methyl-methyl-2κC-[1(η5-pentamethylcyclopentadienyl]galliumtitanium(III, [GaTi(CH33(C10H15(C15H18], are reported. Reacting a dinuclear nitrogen-bridged low-valent titanium(III complex with the Lewis acids AlMe3 or GaMe3 results in the loss of molecular dinitrogen and the formation of two monomeric titanocene(III fragments bearing two μ2-bridging methyl groups. Single crystal X-ray diffraction reveals the formation of a new E—C bond involving the pentafulvene ligand while the bridging and terminal methyl groups remain intact.

  6. Crystal structure of human protein kinase CK2

    DEFF Research Database (Denmark)

    Niefind, K; Guerra, B; Ermakowa, I

    2001-01-01

    The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalyt...... as a docking partner for various protein kinases. Furthermore it shows an inter-domain mobility in the catalytic subunit known to be functionally important in protein kinases and detected here for the first time directly within one crystal structure.......The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalytic...... subunits, which make no direct contact with one another. Each catalytic subunit interacts with both regulatory chains, predominantly via an extended C-terminal tail of the regulatory subunit. The CK2 structure is consistent with its constitutive activity and with a flexible role of the regulatory subunit...

  7. High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

    2013-11-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

  8. Structure of a stacked anthraquinone–DNA complex

    Science.gov (United States)

    De Luchi, Daniela; Usón, Isabel; Wright, Glenford; Gouyette, Catherine; Subirana, Juan A.

    2010-01-01

    The crystal structure of the telomeric sequence d(UBrAGG) interacting with an anthraquinone derivative has been solved by MAD. In all previously studied complexes of intercalating drugs, the drug is usually sandwiched between two DNA base pairs. Instead, the present structure looks like a crystal of stacked anthraquinone molecules in which isolated base pairs are intercalated. Unusual base pairs are present in the structure, such as G·G and A·UBr reverse Watson–Crick base pairs. PMID:20823516

  9. The Role of Coulomb Interactions for Spin Crossover Behaviors and Crystal Structural Transformation in Novel Anionic Fe(III Complexes from a π-Extended ONO Ligand

    Directory of Open Access Journals (Sweden)

    Suguru Murata

    2016-05-01

    Full Text Available To investigate the π-extension effect on an unusual negative-charged spin crossover (SCO FeIII complex with a weak N2O4 first coordination sphere, we designed and synthesized a series of anionic FeIII complexes from a π-extended naphthalene derivative ligand. Acetonitrile-solvate tetramethylammonium (TMA salt 1 exhibited an SCO conversion, while acetone-solvate TMA salt 2 was in a high-spin state. The crystal structural analysis for 2 revealed that two-leg ladder-like cation-anion arrays derived from π-stacking interactions between π-ligands of the FeIII complex anion and Coulomb interactions were found and the solvated acetone molecules were in one-dimensional channels between the cation-anion arrays. A desolvation-induced single-crystal-to-single-crystal transformation to desolvate compound 2’ may be driven by Coulomb energy gain. Furthermore, the structural comparison between quasi-polymorphic compounds 1 and 2 revealed that the synergy between Coulomb and π-stacking interactions induces a significant distortion of coordination structure of 2.

  10. Synthesis and IR spectral study of MoO2Cl2 molecular complex with acetoacetanilides. Crystal structure of MoO2Cl2 complex with acetoacet-2-toluidine

    International Nuclear Information System (INIS)

    Abramenko, V.L.; Sergienko, V.S.; Churakov, A.V.

    2000-01-01

    Certain MoO 2 Cl 2 complexes with acetoacetanilide derivatives were synthesized, two IR spectral study being performed. Crystal and molecular structure of MoO 2 Cl 2 complex with acetoacet-2-toluidine (HL) was determined using X-ray diffraction analysis. The crystals are monoclinic, a = 7.621 (7), b = 9.498 (3), c = 19.980 (9) A, β = 95.16 (7), Z = 4, sp.gr. P2 1 /n. Coordination polyhedron of Mo atom is a distorted octahedron with two O oxoatoms in cis-position, two Cl atom in mutual trans-position and two O(HL) atoms in trans-positions in reference to O(oxo) [ru

  11. Crystal structures of the UBX domain of human UBXD7 and its complex with p97 ATPase.

    Science.gov (United States)

    Li, Zhi-Hui; Wang, Yong; Xu, Min; Jiang, Tao

    2017-04-22

    In humans, UBXD7 (also called UBXN7), an adaptor of p97 ATPase, can participate in the degradation of misfolded or damaged proteins in the p97-mediated ubiquitin proteasome system (UPS). UBXD7 binds to ubiquitinated substrates via its UBA domain and interacts with p97 N-terminal domain through its UBX domain to recruit p97 or the p97 core complex (p97/NPL4/UFD1). Here, we report the crystal structures of the UBX domain of UBXD7 (UBXD7 UBX ) at 2.0 Å resolution and its complex with p97 N-terminal domain (p97 NTD -UBXD7 UBX complex) at 2.4 Å resolution. A structural analysis and isothermal titration calorimetry results provide detailed molecular basis of interaction between UBXD7 UBX and p97 NTD . Moreover, structural superpositions suggest that dimerization of UBXD7 UBX via an intermolecular disulfide bond could interfere with the formation of the p97 NTD -UBXD7 UBX complex. Interestingly, UBXD7 may have a cooperative effect on p97 interaction with UFD1. Together, these results provide structural and biochemical insights into the interaction between p97 NTD and UBXD7 UBX . Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Crystal structure of the Msx-1 homeodomain/DNA complex.

    Science.gov (United States)

    Hovde, S; Abate-Shen, C; Geiger, J H

    2001-10-09

    The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

  13. Synthesis and crystal structure analysis of uranyl triple acetates

    Energy Technology Data Exchange (ETDEWEB)

    Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Serezhkina, Larisa B.; Serezhkin, Victor N. [Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Alekseev, Evgeny V., E-mail: e.alekseev@fz-juelich.de [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)

    2016-12-15

    Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.

  14. Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor.

    Science.gov (United States)

    Underwood, Christina Rye; Garibay, Patrick; Knudsen, Lotte Bjerre; Hastrup, Sven; Peters, Günther H; Rudolph, Rainer; Reedtz-Runge, Steffen

    2010-01-01

    GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic beta-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain in complex with the competitive antagonist exendin-4(9-39). Interestingly, the isolated extracellular domain binds exendin-4 with much higher affinity than the endogenous agonist GLP-1. Here, we have solved the crystal structure of the extracellular domain in complex with GLP-1 to 2.1 Aresolution. The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist- and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous alpha-helix from Thr(13) to Val(33) when bound to the extracellular domain. We supplemented the crystal structure with site-directed mutagenesis to link the structural information of the isolated extracellular domain with the binding properties of the full-length receptor. The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor.

  15. Syntheses, crystal structures and properties of novel copper(II) complexes obtained by reactions of copper(II) sulfate pentahydrate with tripodal ligands.

    Science.gov (United States)

    Zhao, Wei; Fan, Jian; Song, You; Kawaguchi, Hiroyuki; Okamura, Taka-aki; Sun, Wei-Yin; Ueyama, Norikazu

    2005-04-21

    Three novel metal-organic frameworks (MOFs), [Cu(1)SO4].H2O (4), [Cu2(2)2(SO4)2].4H2O (5) and [Cu(3)(H2O)]SO4.5.5H2O (6), were obtained by hydrothermal reactions of CuSO4.5H2O with the corresponding ligands, which have different flexibility. The structures of the synthesized complexes were determined by single-crystal X-ray diffraction analyses. Complex 4 has a 2D network structure with two types of metallacycles. Complex 5 also has a 2D network structure in which each independent 2D sheet contains two sub-layers bridged by oxygen atoms of the sulfate anions. Complex 6 has a 2D puckered structure in which the sulfate anions serve as counter anions, which are different from those in complexes 4 (terminators) and 5 (bridges). The different structures of complexes 4, 5 and 6 indicate that the nature of organic ligands affected the structures of the assemblies greatly. The magnetic behavior of complex 5 and anion-exchange properties of complex 6 were investigated.

  16. Synthesis, crystal structures and thermodynamic properties of two novel lanthanide complexes based on 3,4-diethoxybenzoic acid and 2,2′-bipyridine

    International Nuclear Information System (INIS)

    Jin, Cheng-Wei; Wang, Ye; Ren, Ning; Geng, Li-Na; Zhang, Jian-Jun

    2016-01-01

    Highlights: • Two novel complexes crystal structures are obtained. • The 1-D chain and 2D layer structures were formed via π–π stacking interactions. • The pathway of thermal decomposition for title complexes were investigated. • The molar heat capacities and thermodynamic functions were calculated. - Abstract: Two binuclear lanthanide complexes [Ln(3,4,-DEOBA) 3 DIPY] 2 DIPY (Ln = Tb (1), Dy (2); 3,4,-DEOBA = 3,4-diethoxybenzoate; DIPY = 2,2′-bipyridine) have been synthesized and characterized. The single crystals of complexes 1 and 2 were obtained. And the two complexes are isostructural with a coordination number of eight to form a distorted square antiprism. Carboxylic groups adopt two modes coordinating with Ln(III) ions: bidentate chelate, and bridging bidentate. Binuclear complexes 1 and 2 are stitched together via π–π stacking interactions to form 1D chain and 2D layer supramolecular structures. The two complexes were characterized by elemental analysis, IR spectra, and powder X-ray diffraction. The luminescence spectra of complexes 1 and 2 show the characteristic emissions of Tb 3+ ( 5 D 4 → 7 F 6-3 ) and Dy 3+ ( 4 F 9/2 → 6 H 15/2 , 6 H 13/2 ). The thermal decomposition mechanisms for title complexes were studied by the technology of TG-FTIR. And the heat capacities of two complexes were measured by DSC in the temperature range from 258.15 to 343.15 K. The smoothed heat capacities and thermodynamic functions for complexes 1 and 2 were calculated by fitted polynomial and thermodynamic equations.

  17. New investigations of the guanine trichloro cuprate(II) complex crystal

    Science.gov (United States)

    Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

    2017-01-01

    Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

  18. Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH.

    Science.gov (United States)

    Qin, Hui-Min; Yamamura, Akihiro; Miyakawa, Takuya; Kataoka, Michihiko; Maruoka, Shintaro; Ohtsuka, Jun; Nagata, Koji; Shimizu, Sakayu; Tanokura, Masaru

    2013-11-01

    Conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 is a member of the aldo-keto reductase (AKR) superfamily and reduces ketopantoyl lactone to d-pantoyl lactone in a NADPH-dependent and stereospecific manner. We determined the crystal structure of CPR-C1.NADPH complex at 2.20 Å resolution. CPR-C1 adopted a triose-phosphate isomerase (TIM) barrel fold at the core of the structure in which Thr25 and Lys26 of the GXGTX motif bind uniquely to the adenosine 2'-phosphate group of NADPH. This finding provides a novel structural basis for NADPH binding of the AKR superfamily. Copyright © 2013 Wiley Periodicals, Inc.

  19. Cyanide bridged hetero-metallic polymeric complexes: Syntheses, vibrational spectra, thermal analyses and crystal structures of complexes [M(1,2-dmi)2Ni(μ-CN)4]n (M = Zn(II) and Cd(II))

    Science.gov (United States)

    Kürkçüoğlu, Güneş Süheyla; Sayın, Elvan; Şahin, Onur

    2015-12-01

    Two cyanide bridged hetero-metallic complexes of general formula, [M(1,2-dmi)2Ni(μ-CN)4]n (1,2-dmi = 1,2-dimethylimidazole and M = Zn(II) or Cd(II)) have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal analyses and elemental analyses. The crystallographic analyses reveal that the complexes, [Zn(1,2-dmi)2Ni(μ-CN)4] (1) and [Cd(1,2-dmi)2Ni(μ-CN)4] (2), have polymeric 2D networks. In the complexes, four cyanide groups of [Ni(CN)4]2- coordinated to the adjacent M(II) ions and distorted octahedral geometries of complexes are completed by two nitrogen atoms of trans 1,2-dmi ligands. The structures of 1 and 2 are similar and linked via intermolecular hydrogen bonding, C-H⋯Ni interactions to give rise to 3D networks. Vibration assignments are given for all the observed bands and the spectral features also supported to the crystal structures of heteronuclear complexes. The FT-IR and Raman spectra of the complexes are very much consistent with the structural data presented.

  20. Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug-binding site

    OpenAIRE

    Handing, Katarzyna B.; Shabalin, Ivan G.; Szlachta, Karol; Majorek, Karolina A.; Minor, Wladek

    2016-01-01

    Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1 ?. Cetirizine is bound in two sites ? a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizi...

  1. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

    Science.gov (United States)

    Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

    2016-04-01

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

  2. Syntheses, crystal structures and spectroscopic properties of copper(II)-tetracyanometallate(II) complexes with nicotinamide and isonicotinamide ligands

    Science.gov (United States)

    Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

    2015-09-01

    Four new one dimensional (1D) cyanide complexes, namely {[Cu(NH3)4(μ-na)][M‧(CN)4]}n and {[Cu(NH3)2(ina)2M‧(μ-CN)2(CN)2]}n (M‧(II) = Pd (1 and 3) or Pt (2 and 4), na:nicotinamide and ina:isonicotinamide) have been synthesized and characterized by elemental, spectral (FT-IR and Raman), and thermal (TG, DTG and DTA) analyses. The crystal structures of complexes 1-3 have been determined by single crystal X-ray diffraction technique. In complexes 1 and 2, na ligand is coordinated to the adjacent Cu(II) ions as a bridging ligand, giving rise to 1D linear cationic chain and the [M‧(CN)4]2- anionic complex acts as a counter ion. Complexes 3 and 4 are also 1D linear chain in which two cyanide ligands bridged neighboring M‧(II) and Cu(II) ions, while ina ligand is coordinated Cu(II) ion through nitrogen atom of pyridine ring. In the complexes, the Cu(II) ions adopt distorted octahedral geometries, while M‧(II) ions are four coordinated with four carbon atoms from cyanide ligands in square-planar geometries. The adjacent chains are further stacked through intermolecular hydrogen bond, Nsbnd Hṡṡṡπ, Csbnd H⋯M‧ and M‧⋯π interactions to form 3D supramolecular networks. Vibration assignments are given for all the observed bands. In addition, thermal stabilities of the compounds are also discussed.

  3. Synthesis, crystal structures, molecular docking and urease inhibition studies of Ni(II) and Cu(II) Schiff base complexes

    Science.gov (United States)

    Sangeeta, S.; Ahmad, K.; Noorussabah, N.; Bharti, S.; Mishra, M. K.; Sharma, S. R.; Choudhary, M.

    2018-03-01

    [Ni(L)2] 1 and [Cu(L)2] 2 [HL = 2-((E)-(2-methoxyphenylimino)methyl)-4,6-dichlorophenol] Schiff base complexes have been successfully synthesized and were characterized by FT-IR, UV-Vis, fluorescence spectroscopy and thermogravimetric analysis. The crystal structures of the two complexes were determined through X-ray crystallography. Its inhibitory activity against Helicobacter pylori urease was evaluated in vitro and showed strong inhibitory activity against H. pylori urease compared with acetohydroxamic acid (IC50 = 42.12 μmolL-1), which is a positive reference. A docking analysis using the AutoDock 4.0 program could explain the inhibitory activity of the complex against urease.

  4. Synthesis, Characterization, Crystal Structure and Antibacterial Activities of Transition Metal(II Complexes of the Schiff Base 2-[(4-Methylphenyliminomethyl]-6-methoxyphenol

    Directory of Open Access Journals (Sweden)

    Guo-Liang Zhao

    2009-05-01

    Full Text Available Five transition metal(II complexes, [ML2Cl2] 1~5, were synthesized from the reaction of MCl2·nH2O (M = Mn, Co, Ni, Cu, Cd and the Schiff base ligand 2-[(4-methylphenyliminomethyl]-6-methoxyphenol (C15H15NO2, L, obtained by condensation of o-vanillin (2-hydroxy-3-methoxybenzaldehyde with p-toluidine. They were characterized by elemental analysis, molar conductance, FT-IR spectra, thermal analysis. The structure of complex 1 was determined by single-crystal X-ray diffraction. Its crystal structure is of monoclinic system, space group P21/c with a = 9.0111(18 Å, b = 11.222(2 Å, c =28.130 (6 Å, α = 90 º, β = 92.29(3 º, γ = 90 º, V = 2867.6(10 Å3, Z = 4. The Mn atom is six-coordinate and displays distorted octahedral geometry.The Schiff base ligand and its complexes have been tested in vitro to evaluate their antibacterial activity against bacteria, viz., Escherichia coli, Staphylococcus aureus and Bacillus subtilis. It has been found that the complexes have higher activity than the corresponding free Schiff base ligand against the same bacteria.

  5. Crystal structure of NTPDase2 in complex with the sulfoanthraquinone inhibitor PSB-071.

    Science.gov (United States)

    Zebisch, Matthias; Baqi, Younis; Schäfer, Petra; Müller, Christa E; Sträter, Norbert

    2014-03-01

    In many vertebrate tissues CD39-like ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) act in concert with ecto-5'-nucleotidase (e5NT, CD73) to convert extracellular ATP to adenosine. Extracellular ATP is a cytotoxic, pro-inflammatory signalling molecule whereas its product adenosine constitutes a universal and potent immune suppressor. Interference with these ectonucleotidases by use of small molecule inhibitors or inhibitory antibodies appears to be an effective strategy to enhance anti-tumour immunity and suppress neoangiogenesis. Here we present the first crystal structures of an NTPDase catalytic ectodomain in complex with the Reactive Blue 2 (RB2)-derived inhibitor PSB-071. In both of the two crystal forms presented the inhibitor binds as a sandwich of two molecules at the nucleoside binding site. One of the molecules is well defined in its orientation. Specific hydrogen bonds are formed between the sulfonyl group and the nucleoside binding loop. The methylphenyl side chain functionality that improved NTPDase2-specificity is sandwiched between R245 and R394, the latter of which is exclusively found in NTPDase2. The second molecule exhibits great in-plane rotational freedom and could not be modelled in a specific orientation. In addition to this structural insight into NTPDase inhibition, the observation of the putative membrane interaction loop (MIL) in two different conformations related by a 10° rotation identifies the MIL as a dynamic section of NTPDases that is potentially involved in regulation of catalysis. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Structural transitions and guest/host complexing of liquid crystal helical nanofilaments induced by nanoconfinement.

    Science.gov (United States)

    Kim, Hanim; Ryu, Seong Ho; Tuchband, Michael; Shin, Tae Joo; Korblova, Eva; Walba, David M; Clark, Noel A; Yoon, Dong Ki

    2017-02-01

    A lamellar liquid crystal (LC) phase of certain bent-core mesogenic molecules can be grown in a manner that generates a single chiral helical nanofilament in each of the cylindrical nanopores of an anodic aluminum oxide (AAO) membrane. By introducing guest molecules into the resulting composite chiral nanochannels, we explore the structures and functionality of the ordered guest/host LC complex, verifying the smectic-like positional order of the fluidic nematic LC phase, which is obtained by the combination of the LC organization and the nanoporous AAO superstructure. The guest nematic LC 4'- n -pentyl-4-cyanobiphenyl is found to form a distinctive fluid layered ordered LC complex at the nanofilament/guest interface with the host 1,3-phenylene bis[4-(4-nonyloxyphenyliminomethyl)benzoate], where this interface contacts the AAO cylinder wall. Filament growth form is strongly influenced by mixture parameters and pore dimensions.

  7. Crystal Structure of Glucagon-like Peptide-1 in Complex with the Extracellular Domain of the Glucagon-like Peptide-1 Receptor*

    Science.gov (United States)

    Underwood, Christina Rye; Garibay, Patrick; Knudsen, Lotte Bjerre; Hastrup, Sven; Peters, Günther H.; Rudolph, Rainer; Reedtz-Runge, Steffen

    2010-01-01

    GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic β-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain in complex with the competitive antagonist exendin-4(9–39). Interestingly, the isolated extracellular domain binds exendin-4 with much higher affinity than the endogenous agonist GLP-1. Here, we have solved the crystal structure of the extracellular domain in complex with GLP-1 to 2.1 Åresolution. The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist- and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous α-helix from Thr13 to Val33 when bound to the extracellular domain. We supplemented the crystal structure with site-directed mutagenesis to link the structural information of the isolated extracellular domain with the binding properties of the full-length receptor. The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor. PMID:19861722

  8. Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Manchi C.M.; Kuppan, Gokulan; Shetty, Nishant D.; Owen, Joshua L.; Ioerger, Thomas R.; Sacchettini, James C. (TAM)

    2009-12-01

    S-adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors are also reported: 3{prime}-keto aristeromycin (ARI), 2-fluoroadenosine, and 3-deazaadenosine. The ARI complex is the first reported structure of SAHH complexed with this inhibitor, and confirms the oxidation of the 3{prime} hydroxyl to a planar keto group, consistent with its prediction as a mechanism-based inhibitor. We demonstrate the in vivo enzyme inhibition activity of the three inhibitors and also show that 2-fluoradenosine has bactericidal activity. While most of the residues lining the ADO-binding pocket are identical between Mtb and human SAHH, less is known about the binding mode of the homocysteine (HCY) appendage of the full substrate. We report the 2.0 {angstrom} resolution structure of the complex of SAHH cocrystallized with SAH. The most striking change in the structure is that binding of HCY forces a rotation of His363 around the backbone to flip out of contact with the 5{prime} hydroxyl of the ADO and opens access to a nearby channel that leads to the surface. This complex suggests that His363 acts as a switch that opens up to permit binding of substrate, then closes down after release of the cleaved HCY. Differences in the entrance to this access channel between human and Mtb SAHH are identified.

  9. Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex

    International Nuclear Information System (INIS)

    Debarnot, Claire; Imbert, Isabelle; Ferron, François; Gluais, Laure; Varlet, Isabelle; Papageorgiou, Nicolas; Bouvet, Mickaël; Lescar, Julien; Decroly, Etienne; Canard, Bruno

    2011-01-01

    The expression, purification and crystallization of the SARS coronavirus nsp16 RNA-cap AdoMet-dependent (nucleoside-2′O)-methyltransferase in complex with its activating factor nsp10 are reported. To date, the SARS coronavirus is the only known highly pathogenic human coronavirus. In 2003, it was responsible for a large outbreak associated with a 10% fatality rate. This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. The crystal structure of nsp16 is unknown. Nsp16 is an RNA-cap AdoMet-dependent (nucleoside-2′-O-)-methyltransferase that is only active in the presence of nsp10. In this paper, the expression, purification and crystallization of nsp10 in complex with nsp16 are reported. The crystals diffracted to a resolution of 1.9 Å resolution and crystal structure determination is in progress

  10. Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site

    International Nuclear Information System (INIS)

    Liu, Zhongchuan; Xie, Tian; Zhong, Qiuping; Wang, Ganggang

    2016-01-01

    The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) in a hole motif has been solved; this novel binding site could be a potential structure-based target for protein engineering of CotA laccase. The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at the bottom of the novel binding site, are essential for the oxidation of ABTS and syringaldazine. Specially, a Thr480Phe variant was identified to be almost 3.5 times more specific for ABTS than for syringaldazine compared with the wild type. These results suggest this novel binding site for ABTS could be a potential target for protein engineering of CotA laccases

  11. Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhongchuan; Xie, Tian [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China); Zhong, Qiuping [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China); University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of (China); Wang, Ganggang, E-mail: wanggg@cib.ac.cn [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China)

    2016-03-24

    The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) in a hole motif has been solved; this novel binding site could be a potential structure-based target for protein engineering of CotA laccase. The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at the bottom of the novel binding site, are essential for the oxidation of ABTS and syringaldazine. Specially, a Thr480Phe variant was identified to be almost 3.5 times more specific for ABTS than for syringaldazine compared with the wild type. These results suggest this novel binding site for ABTS could be a potential target for protein engineering of CotA laccases.

  12. Chemistry and structure of technetium complexes

    International Nuclear Information System (INIS)

    Baldas, J.; Boas, J.F.; Bonnyman, J.; Williams, G.A.

    1983-01-01

    The structures of tris(2-aminobenzenethiolato) technetium(VI) and dichlorobis(diethyldithiocarbamato) thionitrosyltechnetium(V) have been determined by single crystal x-ray diffraction analysis. The preparation and chemistry of thiocyanato complexes of technetium have been investigated

  13. Crystal Structure of the Conserved Herpes Virus Fusion Regulator Complex gH–gL

    Energy Technology Data Exchange (ETDEWEB)

    Chowdary, T.; Cairns, T; Atanasiu, D; Cohen, G; Eisenberg, R; Heldwein, E

    2010-01-01

    Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH-gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH-gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, we propose that gH-gL activates gB for fusion, possibly through direct binding. Formation of a gB-gH-gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB-gH-gL interface a promising antiviral target.

  14. Crystal structure of the conserved herpes virus fusion regulator complex gH-gL

    Energy Technology Data Exchange (ETDEWEB)

    Chowdary, Tirumala K; Cairns, Tina M; Atanasiu, Doina; Cohen, Gary H; Eisenberg, Roselyn J; Heldwein, Ekaterina E [UPENN; (Tufts-MED)

    2010-09-13

    Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH-gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH-gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, we propose that gH-gL activates gB for fusion, possibly through direct binding. Formation of a gB-gH-gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB-gH-gL interface a promising antiviral target.

  15. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Guiqing; Sun, Dawei; Rajashankar, Kanagalaghatta R.; Qian, Zhaohui; Holmes, Kathryn V.; Li, Fang (Cornell); (UMM-MED); (Colorado)

    2011-09-28

    Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same {beta}-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusive protein-protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the {beta}-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.

  16. RADCHARM++: A C++ routine to compute the electromagnetic radiation generated by relativistic charged particles in crystals and complex structures

    Energy Technology Data Exchange (ETDEWEB)

    Bandiera, Laura; Bagli, Enrico; Guidi, Vincenzo [INFN Sezione di Ferrara and Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Ferrara, Via Saragat 1, 44121 Ferrara (Italy); Tikhomirov, Victor V. [Research Institute for Nuclear Problems, Belarusian State University, Minsk (Belarus)

    2015-07-15

    The analytical theories of coherent bremsstrahlung and channeling radiation well describe the process of radiation generation in crystals under some special cases. However, the treatment of complex situations requires the usage of a more general approach. In this report we present a C++ routine, named RADCHARM++, to compute the electromagnetic radiation emitted by electrons and positrons in crystals and complex structures. In the RADCHARM++ routine, the model for the computation of e.m. radiation generation is based on the direct integration of the quasiclassical formula of Baier and Katkov. This approach allows one taking into account real trajectories, and thereby the contribution of incoherent scattering. Such contribution can be very important in many cases, for instance for electron channeling. The generality of the Baier–Katkov operator method permits one to simulate the electromagnetic radiation emitted by electrons/positrons in very different cases, e.g., in straight, bent and periodically bent crystals, and for different beam energy ranges, from sub-GeV to TeV and above. The RADCHARM++ routine has been implemented in the Monte Carlo code DYNECHARM++, which solves the classical equation of motion of charged particles traveling through a crystal under the continuum potential approximation. The code has proved to reproduce the results of experiments performed at the MAinzer MIkrotron (MAMI) with 855 MeV electrons and has been used to predict the radiation spectrum generated by the same electron beam in a bent crystal.

  17. INTRAMOLECULAR ALKOXIDE-TETHERED PERMETHYLTITANOCENE(III) COMPLEXES - SYNTHESIS AND CRYSTAL STRUCTURE

    Czech Academy of Sciences Publication Activity Database

    Varga, V.; Císařová, I.; Horáček, Michal; Pinkas, Jiří; Kubišta, Jiří; Mach, Karel

    2009-01-01

    Roč. 74, č. 3 (2009), s. 453-468 ISSN 0010-0765 R&D Projects: GA MPO FT-TA3/078; GA MŠk(CZ) LC06070 Institutional research plan: CEZ:AV0Z40400503 Keywords : titanocene * Permethyltitanocene * crystal structure Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 0.856, year: 2009

  18. Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.

    Science.gov (United States)

    Johnson, Jennifer L; Entzminger, Kevin C; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P; Morales, Ivan A; Sheppard, Aly; Gumbart, James C; Maynard, Jennifer A; Lieberman, Raquel L

    2015-04-01

    Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.

  19. Crystal structure and crystal growth of the polar ferrimagnet CaBaFe4O7

    Science.gov (United States)

    Perry, R. S.; Kurebayashi, H.; Gibbs, A.; Gutmann, M. J.

    2018-05-01

    Magnetic materials are a cornerstone for developing spintronic devices for the transport of information via magnetic excitations. To date, relatively few materials have been investigated for the purpose of spin transport, mostly due to the paucity of suitable candidates as these materials are often chemically complex and difficult to synthesize. We present the crystal growth and a structure solution on the high-temperature crystal structure of the layered, polar ferrimagnet CaBaFe4O7 , which is a possible new contender for spintronics research. The space group is identified as P 3 by refinement of single crystal and powder neutron diffraction data. At 400 K, the trigonal lattice parameters are a =11.0114 (11 )Å and c =10.330 (3 )Å . The structure is similar to the low-temperature phase with alternating layers of triangular and Kagome-arranged Fe-O tetrahedra. We also present details of the crystal growth by traveling solvent method.

  20. Non-covalent interactions in 2-methylimidazolium copper(II) complex (MeImH)2[Cu(pfbz)4]: Synthesis, characterization, single crystal X-ray structure and packing analysis

    Science.gov (United States)

    Sharma, Raj Pal; Saini, Anju; Kumar, Santosh; Kumar, Jitendra; Sathishkumar, Ranganathan; Venugopalan, Paloth

    2017-01-01

    A new anionic copper(II) complex, (MeImH)2 [Cu(pfbz)4] (1) where, MeImH = 2-methylimidazolium and pfbz = pentafluorobenzoate has been isolated by reacting copper(II) sulfate pentahydrate, pentafluorobenzoic acid and 2-methylimidazole in ethanol: water mixture in 1:2:2 molar ratio. This complex 1 has been characterized by elemental analysis, thermogravimetric analysis, spectroscopic techniques (UV-Vis, FT-IR) and conductance measurements. The complex salt crystallizes in monoclinic crystal system with space group C2/c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Cu(pfbz)4]2- anion and two 2-methylimidazolium cation (C4H7N2)+. The crystal lattice is stabilized by strong hydrogen bonding and F⋯F interactions between cationic-anionic and the anionic-anionic moieties respectively, besides π-π interactions.

  1. Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites.

    OpenAIRE

    Kim, M J; Yamamoto, D; Matsumoto, K; Inoue, M; Ishida, T; Mizuno, H; Sumiya, S; Kitamura, K

    1992-01-01

    In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] ...

  2. Crystal structure analysis of human serum albumin complexed with sodium 4-phenylbutyrate.

    Science.gov (United States)

    Kawai, Akito; Yamasaki, Keishi; Enokida, Taisuke; Miyamoto, Shuichi; Otagiri, Masaki

    2018-03-01

    Sodium 4-phenylbutyrate (PB) is an orphan drug for the treatment of urea cycle disorders. It also inhibits the development of endoplasmic reticulum stress, the action of histone deacetylases and as a regulator of the hepatocanalicular transporter. PB is generally considered to have the potential for use in the treatment of the diseases such as cancer, neurodegenerative diseases and metabolic diseases. In a previous study, we reported that PB is primarily bound to human serum albumin (HSA) in plasma and its binding site is drug site 2. However, details of the binding mode of PB to HSA remain unknown. To address this issue, we examined the crystal structure of HSA with PB bound to it. The structure of the HSA-PB complex indicates that the binding mode of PB to HSA is quite similar to that for octanoate or drugs that bind to drug site 2, as opposed to that for other medium-chain length of fatty acids. These findings provide useful basic information related to drug-HSA interactions. Moreover, the information presented herein is valuable in terms of providing safe and efficient treatment and diagnosis in clinical settings.

  3. Nitrido-technetium(V) complexes with amino acids: Preparation and X-ray crystal structure of the L-cysteinate ethyl ester technetium(V) complex

    International Nuclear Information System (INIS)

    Marchi, A.; Rossi, R.; Marvelli, L.; Bertolasi, V.

    1993-01-01

    Technetium-99m is the radionuclide of choice in diagnostic nuclear medicine due to its ideal photon energy of 140 keV and half-life of 6 h. Neutral, stable, and lipophilic technetium complexes with diamino dithiol ligands (DADT) have been widely studied as potential brain perfusion agents and a 99m Tc complex of N,N'-1,2-ethylenediylbis(L-cysteine diethyl ester) (L,L-ECD) has been proposed as a marker of regional cerebral blood flow. It crosses the blood brain barrier (BBB) and is retained in the brain owing to enzymatic hydrolysis of one ester group yielding to a more polar species. More recently, 99m Tc-cysteine complex has been evaluated in animal distribution studies for tumor diagnosis, but its chemical structure has not been determined. A large number of transition metal complexes with amino acids and peptides have been synthesized and structurally characterized to understand their interactions with proteins and antibodies, as well as biocatalytic processes, but only a limited number of rhenium and technetium compounds have been reported. Up to now, the only technetium complex to be characterized by X-ray analysis that contains amino acids as ligand is [TcO(L,L-ECD)]. The author's interest in the nitrido-technetium chemistry is due to the discovery of a new method for preparing radiopharmaceuticals containing the [ 99m Tc triple-bond N] 2+ core. In this communication the authors report the synthesis and characterization of nitrido-technetium complexes with L-cysteine ethyl ester (CYS-OEt), L-cysteine (CYS) and cysteamine (CSA) and the first X-ray crystal structure of a [TcN] 2+ -amino acid complex

  4. Crystal structures of dioxonium hexafluorotantalate and dioxonium hexafluoroniobate complexes with tetrabenzo-30-crown-10

    Energy Technology Data Exchange (ETDEWEB)

    Furmanova, N. G., E-mail: furm@ns.crys.ras.ru; Rabadanov, M. Kh.; Chernaya, T. S. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Fonari, M. S., E-mail: fonari.xray@phys.asm.md; Simonov, Yu. A. [Academy of Sciences of Moldova, Institute of Applied Physics (Moldova, Republic of); Ganin, E. V., E-mail: edganin@yahoo.com [Ministry of Education and Science and National Academy of Sciences of Ukraine, Odessa State Environmental University (Ukraine); Gelmboldt, V. O., E-mail: eksvar@ukr.net [Ministry of Education and Science and National Academy of Sciences of Ukraine, Physicochemical Institute for Human and Environmental Protection (Ukraine); Grigorash, R. Ya.; Kotlyar, S. A.; Kamalov, G. L., E-mail: kamalov@ukr.net.ua [National Academy of Sciences of Ukraine, Bogatsky Physicochemical Institute (Ukraine)

    2008-03-15

    Two isostructural complexes of dioxonium [H{sub 5}O{sub 2}]{sup +} with tetrabenzo-30-crown-10 of the compositions [(tetrabenzo-30-crown-10 {center_dot} H{sub 5}O{sub 2})][TaF{sub 6}] (I) and [(tetrabenzo-30-crown-10 {center_dot} H{sub 5}O{sub 2})][NbF{sub 6}] (II) are studied using X-ray diffraction. The complexes crystallize in the monoclinic crystal system (space group C2/c, Z = 4). The unit cell parameters of these compounds are as follows: a = 15.6583(12) Angstrom-Sign , b = 15.2259(13) Angstrom-Sign , c = 16.4473(13) Angstrom-Sign , and {beta} = 99.398(6) Degree-Sign for complex I and a = 15.7117(12) Angstrom-Sign , b = 15.2785(15) Angstrom-Sign , c = 16.5247(15) Angstrom-Sign , and {beta} = 99.398(7) Degree-Sign for complex II. These complexes belong to the ionic type. The dioxonium cation [H{sub 5}O{sub 2}]{sup +} in the form of the two-unit cluster [H{sub 3}O {center_dot} H{sub 2}O]{sup +} is stabilized by the strong hydrogen bond OH Midline-Horizontal-Ellipsis O [O Midline-Horizontal-Ellipsis O, 2.353(4) Angstrom-Sign ] and encapsulated by the crown ether. Each oxygen atom of the dioxonium cation also forms two oxygen bonds O Midline-Horizontal-Ellipsis O(crown). The crown ether adopts an unusual two-level (pocket-like) conformation, which provides a complete encapsulation of the oxonium associate. The interaction of the cationic complex with the anion in the crystal occurs through contacts of the C-H Midline-Horizontal-Ellipsis F type.

  5. Synthesis and Crystal Structures of Ni(II)/(III) and Zn(II) Complexes with Schiff Base Ligands

    International Nuclear Information System (INIS)

    Koo, Bon Kweon

    2013-01-01

    Coordination polymers are of great interest due to their intriguing structural motifs and potential applications in optical, electronic, magnetic, and porous materials. The most commonly used strategy for designing such materials relies on the utilization of multidentate N- or Odonor ligands which have the capacity to bridge between metal centers to form polymeric structures. The Schiff bases with N,O,S donor atoms are an useful source as they are readily available and easily form stable complexes with most transition metal ions. Schiff bases are also important intermediates in synthesis of some bioactive compounds and are potent anti-bacterial, anti-fungal, anticancer and antiviral compounds. In this work, the Schiff bases, Hapb and Hbpb, derived from 2-acetylpyridene or 2-benzoylpyridine and benzhydrazide were taken as trifunctional (N,N,O) monobasic ligand (Scheme 1). This ligand is of important because the π-delocalization of charge and the configurational flexibility of their molecular chain can give rise to a great variety of coordination modes. Although many metal.Schiff base complexes have been reported, the 1D, 2D, and 3D networks of coordination polymers linked through the bridging of ligands such as dicyanamide, N(CN) 2 - as coligand have been little published. In the process of working to extend the dimensionality of the metal-Schiff base complexes using benzilic acid as a bridging ligand, we obtained three simple metal (II)/(III) complexes of acetylpyridine/2-benzoyl pyridine based benzhydrazide ligand. Therefore, we report here the synthesis and crystal structures of the complexes

  6. SYNTHESIS AND CRYSTAL STRUCTURE OF A NA(I COMPLEX WITH 4,4’-BIPYRIDINE AND 2-FORMYL- BENZENESULFONATE-HYDRAZINE

    Directory of Open Access Journals (Sweden)

    TAI XI-SHI

    2015-07-01

    Full Text Available A Na(I complex, [Na(4,4’-bipyridine2·(H2O4]·L·OH·2H2O (L = 2-formyl-benzenesulfonate-hydrazine, has been synthesized. And its structure was determined by X-ray single crystal diffraction analysis. The Na(I complex belongs to orthorhombic, space group C2221 with a = 7.9162(16 Å, b = 18.451(4 Å, c = 26.397(5 Å, V= 3855.7(13 Å3, Z = 4, Dc = 1.394 mg·m-3, μ = 0.218 mm-1, F(000 =1689, and final R1 = 0.0683, ωR2 = 0.2017. The result shows that the Na(I center is six-coordination with a N2O4 distorted octahedral coordination environment. The Na(I complex forms 1D chain structure by the π-π stacking interaction.

  7. Crystal Structure of the Human Symplekin-Ssu72-CTD Phosphopeptide Complex

    Energy Technology Data Exchange (ETDEWEB)

    K Xiang; T Nigaike; S Xiang; T Kilic; M Beh; J Manley; L Tong

    2011-12-31

    Symplekin (Pta1 in yeast) is a scaffold in the large protein complex that is required for 3'-end cleavage and polyadenylation of eukaryotic messenger RNA precursors (pre-mRNAs); it also participates in transcription initiation and termination by RNA polymerase II (Pol II). Symplekin mediates interactions between many different proteins in this machinery, although the molecular basis for its function is not known. Here we report the crystal structure at 2.4 {angstrom} resolution of the amino-terminal domain (residues 30-340) of human symplekin in a ternary complex with the Pol II carboxy-terminal domain (CTD) Ser5 phosphatase Ssu72 and a CTD Ser5 phosphopeptide. The N-terminal domain of symplekin has the ARM or HEAT fold, with seven pairs of antiparallel {alpha}-helices arranged in the shape of an arc. The structure of Ssu72 has some similarity to that of low-molecular-mass phosphotyrosine protein phosphatase, although Ssu72 has a unique active-site landscape as well as extra structural features at the C terminus that are important for interaction with symplekin. Ssu72 is bound to the concave face of symplekin, and engineered mutations in this interface can abolish interactions between the two proteins. The CTD peptide is bound in the active site of Ssu72, with the pSer5-Pro6 peptide bond in the cis configuration, which contrasts with all other known CTD peptide conformations. Although the active site of Ssu72 is about 25 {angstrom} from the interface with symplekin, we found that the symplekin N-terminal domain stimulates Ssu72 CTD phosphatase activity in vitro. Furthermore, the N-terminal domain of symplekin inhibits polyadenylation in vitro, but only when coupled to transcription. Because catalytically active Ssu72 overcomes this inhibition, our results show a role for mammalian Ssu72 in transcription-coupled pre-mRNA 3'-end processing.

  8. Crystal structure of the C3bot–RalA complex reveals a novel type of action of a bacterial exoenzyme

    OpenAIRE

    Pautsch, Alexander; Vogelsgesang, Martin; Tränkle, Jens; Herrmann, Christian; Aktories, Klaus

    2005-01-01

    C3 exoenzymes from bacterial pathogens ADP-ribosylate and inactivate low-molecular-mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP-ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD-glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP-bou...

  9. High-resolution diffraction from crystals of a membrane-protein complex: bacterial outer membrane protein OmpC complexed with the antibacterial eukaryotic protein lactoferrin

    International Nuclear Information System (INIS)

    Sundara Baalaji, N.; Acharya, K. Ravi; Singh, T. P.; Krishnaswamy, S.

    2005-01-01

    Crystals of the complex formed between the bacterial membrane protein OmpC and the antibacterial protein lactoferrin suitable for high-resolution structure determination have been obtained. The crystals belong to the hexagonal space group P6, with unit-cell parameters a = b = 116.3, c = 152.4 Å. Crystals of the complex formed between the outer membrane protein OmpC from Escherichia coli and the eukaryotic antibacterial protein lactoferrin from Camelus dromedarius (camel) have been obtained using a detergent environment. Initial data processing suggests that the crystals belong to the hexagonal space group P6, with unit-cell parameters a = b = 116.3, c = 152.4 Å, α = β = 90, γ = 120°. This indicated a Matthews coefficient (V M ) of 3.3 Å 3 Da −1 , corresponding to a possible molecular complex involving four molecules of lactoferrin and two porin trimers in the unit cell (4832 amino acids; 533.8 kDa) with 63% solvent content. A complete set of diffraction data was collected to 3 Å resolution at 100 K. Structure determination by molecular replacement is in progress. Structural study of this first surface-exposed membrane-protein complex with an antibacterial protein will provide insights into the mechanism of action of OmpC as well as lactoferrin

  10. The Crystal Structure of a High-Spin Oxoiron(IV) Complex and Characterization of Its Self-Decay Pathway

    Energy Technology Data Exchange (ETDEWEB)

    England, J.; Guo, Y; Farquhar, E; Young, Jr., V; Münck, E; Que, Jr., L

    2010-01-01

    [Fe{sup IV}(O)(TMG{sub 3}tren)]{sup 2+} (1; TMG{sub 3}tren = 1,1,1-tris{l_brace}2-[N{sup 2}-(1,1,3,3-tetramethylguanidino)]ethyl{r_brace}amine) is a unique example of an isolable synthetic S = 2 oxoiron(IV) complex, which serves as a model for the high-valent oxoiron(IV) intermediates observed in nonheme iron enzymes. Congruent with DFT calculations predicting a more reactive S = 2 oxoiron(IV) center, 1 has a lifetime significantly shorter than those of related S = 1 oxoiron(IV) complexes. The self-decay of 1 exhibits strictly first-order kinetic behavior and is unaffected by solvent deuteration, suggesting an intramolecular process. This hypothesis was supported by ESI-MS analysis of the iron products and a significant retardation of self-decay upon use of a perdeuteromethyl TMG{sub 3}tren isotopomer, d{sub 36}-1 (KIE = 24 at 25 C). The greatly enhanced thermal stability of d{sub 36}-1 allowed growth of diffraction quality crystals for which a high-resolution crystal structure was obtained. This structure showed an Fe=O unit (r = 1.661(2) {angstrom}) in the intended trigonal bipyramidal geometry enforced by the sterically bulky tetramethylguanidinyl donors of the tetradentate tripodal TMG{sub 3}tren ligand. The close proximity of the methyl substituents to the oxoiron unit yielded three symmetrically oriented short C-D {hor_ellipsis} O nonbonded contacts (2.38-2.49 {angstrom}), an arrangement that facilitated self-decay by rate-determining intramolecular hydrogen atom abstraction and subsequent formation of a ligand-hydroxylated iron(III) product. EPR and Moessbauer quantification of the various iron products, referenced against those obtained from reaction of 1 with 1,4-cyclohexadiene, allowed formulation of a detailed mechanism for the self-decay process. The solution of this first crystal structure of a high-spin (S = 2) oxoiron(IV) center represents a fundamental step on the path toward a full understanding of these pivotal biological intermediates.

  11. Six-coordinate oxo-vanadium(V) dimer complex with methoxy bridging: synthesis, crystal structure, biological activity and molecular docking

    Czech Academy of Sciences Publication Activity Database

    Heidari, F.; Fatemi, S.J.A.; Yousef Ebrahimipour, S.; Ebrahimnejad, H.; Castro, J.; Dušek, Michal; Eigner, Václav

    2017-01-01

    Roč. 76, Feb (2017), s. 1-4 ISSN 1387-7003 R&D Projects: GA MŠk(CZ) LO1603; GA ČR(CZ) GA14-03276S EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : oxo-vanadium(V) * Schiff base complex * antimicrobial activity * X-ray crystal structure Subject RIV: CA - Inorganic Chemistry OBOR OECD: Inorganic and nuclear chemistry Impact factor: 1.640, year: 2016

  12. Synthesis, characterization, X-ray crystal structure and conductometry studying of a number of new Schiff base complexes; a new example of binuclear square pyramidal geometry of Cu(II) complex bridged with an oxo group

    Science.gov (United States)

    Golbedaghi, Reza; Alavipour, Ehsan

    2015-11-01

    Three new binuclear Cu(II), Mn(II), Co(II) complexes [Cu2(L) (ClO4)](ClO4)2 (1), [Mn2(L) (ClO4)](ClO4)2 (2), and [Co2(L) (ClO4)](ClO4)2 (3), {L = 1,3-bis(2-((Z)-(2-aminopropylimino)methyl)phenoxy)propan-2-ol} have been synthesized. Single crystal X-ray structure analysis of complex 1 showed that the complex is binuclear and all nitrogen and oxygen atoms of ligand (N4O3) are coordinated to two Cu(II) center ions. In addition, the crystal structure studying shows, a perchlorate ion has been bridged to the Cu(II) metal centers. However, two distorted square pyramidal Cu(II) ions are bridged asymmetrically by a perchlorate ion and oxygen of hydroxyl group of Schiff base ligand. In addition, the conductometry behaviors of all complexes were studied in acetonitrile solution.

  13. Halide/pseudohalide complexes of cadmium(II) with benzimidazole: Synthesis, crystal structures and fluorescence properties

    Science.gov (United States)

    Zhao, Hai-Yan; Yang, Fu-Li; Li, Na; Wang, Xiao-Jing

    2017-11-01

    Two new dinuclear Cd(II) complexes, [CdL1Cl2]2·H2O (1) and [CdL1(N3)2]2·CH3OH (2) and one dicyanamide bridged one-dimensional polynuclear network [CdL1(μ1,5-dca)dca]n (3) of the potentially tridentate NNN-donor Schiff base 2-((1H-benzimidazol-2-yl-ethylimino)-methyl)pyridine (L1) and another dinucler Cd(II) complex [CdL2Cl(dca)]2 (4) of a similar NNN-donor Schiff base ligand 2-((1H-benzimidazol-2-yl-propylimino)-methyl)pyridine (L2), have been synthesized and characterized by elemental analyses, IR and single crystal X-ray crystallography. The ligands L1 and L2 are [1 + 1] condensation products of pyridine-2-carbaldehyde with 2-aminoethyl-1H-benzimidazole and 2-aminopropyl-1H-benzimidazole, respectively. In the complexes 1 and 4 the two Cd(II) centers are held together by the bridged chloride ligands, while in 2 the two Cd(II) centers are bridged by μ1,1-azide ions. Complex 3 has a one-dimensional infinite chain structure in which Cd(II) ions are bridged by single dicyanamide groups in end-to-end fashion. All the metal centers have a distorted octahedral geometry and H-bonding or π⋯π interactions are operative to bind the complex units in the solid state. Furthermore, these complexes have been investigated by thermogravimetric analyses and fluorescence spectra.

  14. Novel polymeric potassium complex: Its synthesis, structural characterization, photoluminescence and electrochemical properties

    Energy Technology Data Exchange (ETDEWEB)

    Ceyhan, Goekhan [Chemistry Department, K.Maras Suetcue Imam University, 46100 K.Maras (Turkey); Tuemer, Mehmet, E-mail: mtumer@ksu.edu.tr [Chemistry Department, K.Maras Suetcue Imam University, 46100 K.Maras (Turkey); Koese, Muhammet; McKee, Vickie [Chemistry Department, Loughborough University, LE11 3TU Leicestershire (United Kingdom)

    2012-03-15

    In this paper, we obtained a novel poly(vanillinato potassium) complex (PVP) as a single crystal and characterized by analytical and spectroscopic methods. A single crystal of the PVP was obtained from the acetone solution. X-ray structural data show that crystals contain polymeric K{sup +} complex of vanillin. Each potassium ion in the polymeric structure is identical and seven-coordinate, bonded to two methoxy, two phenoxy and three aldehyde oxygen atoms from four vaniline molecules. Two aldehyde oxygen atoms are bridging between potassium ions. It crystallizes in the monoclinic system, space group P2{sub 1}/c, with lattice parameters a=9.6215(10) A, b=17.4139(19) A, c=9.6119(10) A, {beta}=100.457(2) Degree-Sign and Z=4. Thermal properties of the PVP were investigated by TGA, DTA and DSC methods. The electrochemical properties of the complex were studied in different solvents and at various scan rates. The luminescence properties of the complex in different solvents and at different pH values have been investigated. The results show that the complex exhibits more efficient luminescence property in CH{sub 3}CN and n-butanol. - Highlights: Black-Right-Pointing-Pointer Novel polymeric potassium complex was prepared and fully characterized. Black-Right-Pointing-Pointer X-ray crystal structure of complex was reported. Black-Right-Pointing-Pointer Electrochemical properties of compound were investigated. Black-Right-Pointing-Pointer Thermal and DSC measurements of complex were examined.

  15. Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda).

    Science.gov (United States)

    Seng, Hoi-Ling; Ong, Han-Kiat Alan; Rahman, Raja Noor Zaliha Raja Abd; Yamin, Bohari M; Tiekink, Edward R T; Tan, Kong Wai; Maah, Mohd Jamil; Caracelli, Ignez; Ng, Chew Hee

    2008-11-01

    The binding selectivity of the M(phen)(edda) (M=Cu, Co, Ni, Zn; phen=1,10-phenanthroline, edda=ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(II) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N(4)O(2) octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling.

  16. Preparations and crystal structures of 8 coordinate uranyl(VI) complexes having macrocyclic ligands derived from pyrroledicarboxialdehydes and diamines

    International Nuclear Information System (INIS)

    Komagine, J.; Takeda, M.; Takahashi, M.

    2006-01-01

    Six 8-coordinate uranyl(VI) complexes with macrocyclic Schiff base ligands derived from 2,6-pyrroledicarboxialdehyde and diamines are prepared and the crystal structures for two of them are determined focusing on the relation between the size of the ligands and U-N bond distances. No difference in average uranyl bond distances and bond angles are observed between [UO 2 (bipytn)](a) and [UO 2 (bipydmtn)](b). U-N bonds of these complexes are, however, not equal; the U-N(pyrrole) bonds [2.45(a), 2.44(b) A] are much shorter than the U-N(imine) bonds [2.67(a), 2.67(b) A]. (author)

  17. Synthesis and crystal structure of the iridium(I) carbene complex with a pair of hydrogen wing tips

    Energy Technology Data Exchange (ETDEWEB)

    Huang, H.-Y.; Chen, Z.-M.; Wang, Y.; Wu, E.-M.; Wang, G. [Jiangsu Institute of Nuclear Medicine, Ministry of Health, Key Laboratory of Molecular Nuclear Medicine (China); Jiang, M.-J., E-mail: jmj16888@126.com [Nanjing Medical University, Affiliated Wuxi Peoples Hospital, Wuxi Institute of Translational Medicine, Department of Clinical Laboratory Science (China)

    2016-12-15

    The iridium(I) cyclooctadiene complex with two (3-tert-butylimidazol-2-ylidene) ligands [(H-Im{sup t}Bu){sub 2}Ir(COD)]{sup +}PF{sub 6}{sup −} (C{sub 22}H{sub 32}PF{sub 6}IrN{sub 4}) has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal atom, which is coordinated by two H-Im{sup t}Bu ligands and one cyclooctadiene group. The new iridium carbene complex has a pair of hydrogen wing tips. The Ir−C{sub carbene} bond lengths are 2.066(5) and 2.052(5) Å, and the bond angle C−Ir−C between these bonds is 95.54(19)°. The dihedral angle between two imidazol-2-ylidene rings is 86.42°.

  18. One-dimensional crystal with a complex periodic potential

    International Nuclear Information System (INIS)

    Boyd, John K.

    2001-01-01

    A one-dimensional crystal model is constructed with a complex periodic potential. A wave function solution for the crystal model is derived without relying on Bloch functions. The new wave function solution of this model is shown to correspond to the solution for the probability amplitude of a two-level system. The energy discriminant is evaluated using an analytic formula derived from the probability amplitude solution, and based on an expansion parameter related to the energy and potential amplitude. From the wave function energy discriminant the crystal band structure is derived and related to standard energy bands and gaps. It is also shown that several of the properties of the two-level system apply to the one-dimensional crystal model. The two-level system solution which evolves in time is shown to manifest as a spatial configuration of the one-dimensional crystal model. The sensitivity of the wave function probability density is interpreted in the context of the new solution. The spatial configuration of the wave function, and the appearance of a long wavelength in the wave function probability density is explained in terms of the properties of Bessel functions

  19. Crystal structure of clathrates of Hofmann dma-type

    International Nuclear Information System (INIS)

    NIshikiori, Sh.; Ivamoto, T.

    1999-01-01

    Seven new clathrates Cd(DMA) 2 Ni(CN) 4 ·xG (x=1, G=aniline, 2,3-xylidine, 2,4-xylidine, 2,5-xylidine, 2,6-xylidine, 3,5-xylidine, and x=2, G=2,4,6-trimethylaniline) of Hofmann type are synthesized by amine substitution for dimethylamine (DMA). On the base of x-ray diffraction data it is shown that geometry of guest molecule in cage-like hollow determines the structure of the host and crystal structure of clathrates. Two-dimension metallocomplex of the host of studied clathrates is characterized by elastic folded structure appearing as a result of angular deformation of bond between Cd atoms and host cyanide bridge. Guest molecule orientation is fixed by hydrogen bond. Structural elasticity of the host complex directs to differences in crystal structure of clathrates formed and to considerable variety of incorporated guests [ru

  20. Crystal structure analysis of human serum albumin complexed with sodium 4-phenylbutyrate

    Directory of Open Access Journals (Sweden)

    Akito Kawai

    2018-03-01

    Full Text Available Sodium 4-phenylbutyrate (PB is an orphan drug for the treatment of urea cycle disorders. It also inhibits the development of endoplasmic reticulum stress, the action of histone deacetylases and as a regulator of the hepatocanalicular transporter. PB is generally considered to have the potential for use in the treatment of the diseases such as cancer, neurodegenerative diseases and metabolic diseases. In a previous study, we reported that PB is primarily bound to human serum albumin (HSA in plasma and its binding site is drug site 2. However, details of the binding mode of PB to HSA remain unknown. To address this issue, we examined the crystal structure of HSA with PB bound to it. The structure of the HSA–PB complex indicates that the binding mode of PB to HSA is quite similar to that for octanoate or drugs that bind to drug site 2, as opposed to that for other medium-chain length of fatty acids. These findings provide useful basic information related to drug–HSA interactions. Moreover, the information presented herein is valuable in terms of providing safe and efficient treatment and diagnosis in clinical settings. Keywords: Human serum albumin, X-ray crystallography, Sodium 4-phenylbutyrate, Drug interaction, Drug site 2

  1. Complex photonic structures

    International Nuclear Information System (INIS)

    Wiersma, D.S.

    2013-01-01

    We discuss in detail the optical properties of complex photonic structures, in particular those with a dominating disorder component. We will focus on their general transport properties, as well as on their use as light sources (random lasers). The basis for the theory of multiple light scattering in random systems will be explained as a tutorial introduction to the topic, including the explicit calculation of the effect of coherent backscattering. We will discuss various structures that go beyond regular disordered ones, in particular Levy glasses, liquid crystals, and quasicrystals, and show examples of their optical properties both from a conceptual and practical point of view.

  2. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Zhiqiang; Su, Lijing; Pei, Jimin; Grishin, Nick V.; Zhang, Hong (UTSMC)

    2017-08-01

    In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.

  3. Synthesis, crystal structure, fluorescence and electrochemical studies of a new tridentate Schiff base ligand and its nickel(II) and palladium(II) complexes

    Science.gov (United States)

    Shafaatian, Bita; Soleymanpour, Ahmad; Kholghi Oskouei, Nasim; Notash, Behrouz; Rezvani, Seyyed Ahmad

    2014-07-01

    A new unsymmetrical tridentate Schiff base ligand was derived from the 1:1 M condensation of ortho-vanillin with 2-mercaptoethylamine. Nickel and palladium complexes were obtained by the reaction of the tridentate Schiff base ligand with nickel(II) acetate tetrahydrate and palladium(II) acetate in 2:1 M ratio. In nickel and palladium complexes the ligand was coordinated to metals via the imine N and enolic O atoms. The S groups of Schiff bases were not coordinated to the metals and S-S coupling was occured. The complexes have been found to possess 1:2 Metal:Ligand stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The complexes exhibited octahedral coordination geometry. The emission spectra of the ligand and its complexes were studied in methanol. Electrochemical properties of the ligand and its metal complexes were investigated in the CH3CN solvent at the 100 mV s-1 scan rate. The ligand and metal complexes showed both reversible and quasi-reversible processes at this scan rate. The Schiff base and its complexes have been characterized by IR, 1H NMR, UV/Vis, elemental analyses and conductometry. The crystal structure of nickel complex has been determined by single crystal X-ray diffraction.

  4. Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting α-glycosidase.

    Science.gov (United States)

    Miyazaki, Takatsugu; Nishikawa, Atsushi; Tonozuka, Takashi

    2016-12-01

    Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1.8- and 2.1-Å resolutions, respectively. Because glucose and lactose molecules are found at the active sites in both structures, it is possible that these structures mimic the enzyme-product complex of YgjK. A glucose molecule found at subsite -1 in both structures adopts an unusual 1 S 3 skew-boat conformation. Comparison between these structures and the previously determined enzyme-substrate complex structure reveals that the glucose pyranose ring might be distorted immediately after nucleophilic attack by a water molecule. These structures represent the first enzyme-product complex for the GH63 family, as well as the structurally-related glycosidases, and it may provide insight into the catalytic mechanism of these enzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Fabrication and characterization of poly(L-lactic acid) gels induced by fibrous complex crystallization with solvents

    Energy Technology Data Exchange (ETDEWEB)

    Matsuda, Yasuhiro [ORNL; Fukatsu, Akinobu [Shizuoka University, Hamamatsu, Japan; Wang, Yangyang [ORNL; Miyamoto, Kazuaki [Shizuoka University, Hamamatsu, Japan; Mays, Jimmy [University of Tennessee, Knoxville (UTK); Tasaka, Shigeru [Shizuoka University, Hamamatsu, Japan

    2014-01-01

    Complex crystal induced gelation of poly(L-lactic acid) (PLLA) solutions was studied for a series of solvents, including N,N-dimethylformamide (DMF). By cooling the solutions prepared at elevated temperatures, PLLA gels were produced in solvents that induced complex crystals ( -crystals) with PLLA. Fibrous structure of PLLA in the gel with DMF was observed by polarizing optical microscopy, field emission electron microscopy, and atomic force microscopy. Upon heating, the crystal form of PLLA in the DMF gel changed from -crystal to a-crystal, the major crystal form in common untreated PLLA films, but the morphology and high elastic modulus of the gel remained until the a-crystal dissolved at higher temperature. In addition, a solvent exchanging method was developed, which allowed PLLA gels to be prepared in other useful solvents that do not induce -crystals without losing the morphology and mechanical properties.

  6. Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (DiaminocarbenePdII Complexes

    Directory of Open Access Journals (Sweden)

    Alexander S. Mikherdov

    2018-02-01

    Full Text Available The coupling of cis-[PdCl2(CNXyl2] (Xyl = 2,6-Me2C6H3 with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbenePdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB. The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D polymeric chains (for 3a,b, dimeric associates (for 3c, or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%, S•••S (3c: less 1%, S•••O (3d: less 1%. The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method, confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry. The AIM analysis demonstrates the presence of appropriate bond critical points for these

  7. Crystal Structure and Substrate Specificity of D-Galactose-6-Phosphate Isomerase Complexed with Substrates

    Science.gov (United States)

    Lee, Jung-Kul; Pan, Cheol-Ho

    2013-01-01

    D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26), which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD), catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi). Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αβα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays. PMID:24015281

  8. Crystal structure and substrate specificity of D-galactose-6-phosphate isomerase complexed with substrates.

    Directory of Open Access Journals (Sweden)

    Woo-Suk Jung

    Full Text Available D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26, which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD, catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi. Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αβα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays.

  9. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Directory of Open Access Journals (Sweden)

    Julien Robert-Paganin

    Full Text Available FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686: one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  10. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Science.gov (United States)

    Robert-Paganin, Julien; Nonin-Lecomte, Sylvie; Réty, Stéphane

    2012-01-01

    FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686): one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  11. One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

    Science.gov (United States)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

    2016-11-01

    Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

  12. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

  13. Thermal neutron detectors based on complex oxide crystals

    CERN Document Server

    Ryzhikov, V; Volkov, V; Chernikov, V; Zelenskaya, O

    2002-01-01

    The ways of improvement of spectrometric quality of CWO and GSO crystals have been investigated with the aim of their application in thermal neutron detectors based on radiation capture reactions. The efficiency of the neutron detection by these crystals was measured, and the obtained data were compared with the results for sup 6 LiI(Tl) crystals. It is shown that the use of complex oxide crystals and neutron-absorption filters for spectrometry of thermal and resonance neutrons could be a promising method in combination with computer data processing. Numerical calculations are reported for spectra of gamma-quanta due to radiation capture of the neutrons. To compensate for the gamma-background lines, we used a crystal pair of heavy complex oxides with different sensitivity to neutrons.

  14. Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions

    International Nuclear Information System (INIS)

    Kiser, Philip D.; Lodowski, David T.; Palczewski, Krzysztof

    2007-01-01

    A 3.02 Å crystal structure of native GroEL from E. coli is presented. GroEL is a member of the ATP-dependent chaperonin family that promotes the proper folding of many cytosolic bacterial proteins. The structures of GroEL in a variety of different states have been determined using X-ray crystallography and cryo-electron microscopy. In this study, a 3.02 Å crystal structure of the native GroEL complex from Escherichia coli is presented. The complex was purified and crystallized in the absence of potassium ions, which allowed evaluation of the structural changes that may occur in response to cognate potassium-ion binding by comparison to the previously determined wild-type GroEL structure (PDB code http://www.rcsb.org/pdb/explore.do?structureId), in which potassium ions were observed in all 14 subunits. In general, the structure is similar to the previously determined wild-type GroEL crystal structure with some differences in regard to temperature-factor distribution

  15. Synthesis, crystal structure and biological activity of the Schiff base organotin(IV) complexes based on salicylaldehyde-o-aminophenol

    Science.gov (United States)

    Tan, Yu-Xing; Zhang, Zhi-Jian; Liu, Yang; Yu, Jiang-Xi; Zhu, Xiao-Ming; Kuang, Dai-Zhi; Jiang, Wu-Jiu

    2017-12-01

    Schiff base organotin(IV) complexes C1 ∼ C5b have been synthesized via the reaction of the substituted salicylaldehyde-o-aminophenol Schiff base ligands (L1 ∼ L3) with the dibenzyltin dichloride, n-butyltin trichloride or dibutyltin oxide, respectively. The complexes have been characterized by IR, UV-Vis, 1H NMR, 13C NMR spectra, elemental analysis and the crystal structures have been determined by X-ray diffraction. The anticancer activity of the Schiff base ligand and complexes C1 ∼ C5b against five species of cancer cell which are Hela, MCF7, HepG2, Colo205, NCIsbnd H460 were tested respectively, the tests showed that C1 ∼ C5b exhibited significant anticancer activity for the cancer cells in comparison with the ligand, and the activity was greater than carboplatin.

  16. Crystal structure of reovirus attachment protein σ1 in complex with sialylated oligosaccharides.

    Science.gov (United States)

    Reiter, Dirk M; Frierson, Johnna M; Halvorson, Elizabeth E; Kobayashi, Takeshi; Dermody, Terence S; Stehle, Thilo

    2011-08-01

    Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.

  17. Crystal structure of reovirus attachment protein σ1 in complex with sialylated oligosaccharides.

    Directory of Open Access Journals (Sweden)

    Dirk M Reiter

    2011-08-01

    Full Text Available Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.

  18. Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate

    International Nuclear Information System (INIS)

    Pauwels, Kris; Loris, Remy; Vandenbussche, Guy; Ruysschaert, Jean-Marie; Wyns, Lode; Van Gelder, Patrick

    2005-01-01

    Crystals of the lipase of B. glumae in complex with its specific foldase were obtained in two forms. Crystallization, crystal manipulation and preliminary X-ray diffraction analysis are described. Bacterial lipases that are secreted via the type II secretion pathway require a lipase-specific foldase in order to obtain their native and biologically active conformation in the periplasmic space. The lipase–foldase complex from Burkholderia glumae (319 and 333 residues, respectively) was crystallized in two crystal forms. One crystal form belongs to space group P3 1 21 (P3 2 21), with unit-cell parameters a = b = 122.3, c = 98.2 Å. A procedure is presented which improved the diffraction of these crystals from ∼5 to 2.95 Å. For the second crystal form, which belonged to space group C2 with unit-cell parameters a = 183.0, b = 75.7, c = 116.6 Å, X-ray data were collected to 1.85 Å

  19. Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kailang; Li, Weikai; Peng, Guiqing; Li, Fang; (Harvard-Med); (UMM-MED)

    2010-03-04

    NL63 coronavirus (NL63-CoV), a prevalent human respiratory virus, is the only group I coronavirus known to use angiotensin-converting enzyme 2 (ACE2) as its receptor. Incidentally, ACE2 is also used by group II SARS coronavirus (SARS-CoV). We investigated how different groups of coronaviruses recognize the same receptor, whereas homologous group I coronaviruses recognize different receptors. We determined the crystal structure of NL63-CoV spike protein receptor-binding domain (RBD) complexed with human ACE2. NL63-CoV RBD has a novel {beta}-sandwich core structure consisting of 2 layers of {beta}-sheets, presenting 3 discontinuous receptor-binding motifs (RBMs) to bind ACE2. NL63-CoV and SARS-CoV have no structural homology in RBD cores or RBMs; yet the 2 viruses recognize common ACE2 regions, largely because of a 'virus-binding hotspot' on ACE2. Among group I coronaviruses, RBD cores are conserved but RBMs are variable, explaining how these viruses recognize different receptors. These results provide a structural basis for understanding viral evolution and virus-receptor interactions.

  20. Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

    Energy Technology Data Exchange (ETDEWEB)

    Linko, R. V., E-mail: rlinko@mail.ru [Peoples' Friendship University of Russia (Russian Federation); Sokol, V. I. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

    2013-05-15

    The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

  1. Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

    International Nuclear Information System (INIS)

    Linko, R. V.; Sokol, V. I.; Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V.; Sergienko, V. S.

    2013-01-01

    The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL 2 ] · CHCl 3 (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL 2 are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

  2. Crystal structures of a manganese(I and a rhenium(I complex of a bipyridine ligand with a non-coordinating benzoic acid moiety

    Directory of Open Access Journals (Sweden)

    Sheri Lense

    2018-05-01

    Full Text Available The structures of two facially coordinated Group VII metal complexes are reported, namely: fac-bromido[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylmanganese(I tetrahydrofuran monosolvate, [MnBr(C17H12N2O2(CO3]·C4H8O, I, and fac-[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylchloridorhenium(I tetrahydrofuran monosolvate, [ReCl(C17H12N2O2(CO3]·C4H8O, II. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ion, and a 2-(2,2′-bipyridin-6-ylbenzoic acid ligand, in a distorted octahedral geometry. In manganese complex I, the tetrahydrofuran (THF solvent molecule could not be refined due to disorder. The benzoic acid fragment is also disordered over two positions, such that the carboxylic acid group is either positioned near to the bromide ligand or to the axial carbonyl ligand. In the crystal of I, the complex molecules are linked by a pair of C—H...Br hydrogen bonds, forming inversion dimers that stack up the a-axis direction. In the rhenium complex II, there is hydrogen bonding between the benzoic acid moiety and a disordered co-crystallized THF molecule. In the crystal, the molecules are linked by C—H...Cl hydrogen bonds, forming layers parallel to (100 separated by layers of THF solvent molecules.

  3. Silver(I) complexes with hydantoins and allantoin: synthesis, crystal and molecular structure, cytotoxicity and pharmacokinetics.

    Science.gov (United States)

    Puszyńska-Tuszkanow, Mariola; Grabowski, Tomasz; Daszkiewicz, Marek; Wietrzyk, Joanna; Filip, Beata; Maciejewska, Gabriela; Cieślak-Golonka, Maria

    2011-01-01

    Coordination polymers [Ag(L(1,3))](n) (L(1)=hydantoin, L(3)=5,5-dimethylhydantoin), {[Ag(L(2))](.)0.5H(2)O}(n) (L(2)=1-methylhydantoin) and [Ag(NH(3))(L(4))](n) (L(4)=allantoin) were prepared and characterized by elemental analysis, spectroscopic (IR, FTIR and NMR), thermal and mass spectrometry methods. The crystal structure of {[Ag(1-methylhydantoin)]·0,5H(2)O}(n) was determined and analyzed. Three 1-methylhydantoinate ligands create a T-shape (CN=3) coordination sphere around the Ag(+) ion. Additionally, a short Ag⋯Ag distance of 2.997Å was found in the structure resulting in the expanded [3+2] environment of a distorted square shape. The [Ag(L(2))] entities are bound to each other by the bridging organic ligands. Thus a two-dimensional coordination polymer is created with water molecules located between the layers. In contrast to hydantoins, the allantoin complex contains an additional ammonia molecule in the coordination sphere. Moreover, in the Ag-alla complex the M-organic ligand binding site is shifted to the N-atom of the ureid chain. Free ligands are cytotoxically inactive against human MCF-7 and A549 cancer cell lines and mouse fibroblasts Balb/3T3. The silver hydantoin complexes exhibit a very strong activity against these lines. (The introduction of the methyl groups to the ring slightly increases resistance only against the A549 cell line.) In contrast, the silver complex of allantoin shows only a weak activity which may be related to the presence of the cytotoxic ammonia group in the composition of the compound and/or the different binding site of the ligand. Calculated in silico physiochemical parameters are promising for the future application of the complexes as drugs. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Structural and Electronic Investigations of Complex Intermetallic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Hyunjin [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

  5. Crystal Structure of Feline Infectious Peritonitis Virus Main Protease in Complex with Synergetic Dual Inhibitors.

    Science.gov (United States)

    Wang, Fenghua; Chen, Cheng; Liu, Xuemeng; Yang, Kailin; Xu, Xiaoling; Yang, Haitao

    2016-02-15

    Coronaviruses (CoVs) can cause highly prevalent diseases in humans and animals. Feline infectious peritonitis virus (FIPV) belongs to the genus Alphacoronavirus, resulting in a lethal systemic granulomatous disease called feline infectious peritonitis (FIP), which is one of the most important fatal infectious diseases of cats worldwide. No specific vaccines or drugs have been approved to treat FIP. CoV main proteases (M(pro)s) play a pivotal role in viral transcription and replication, making them an ideal target for drug development. Here, we report the crystal structure of FIPV M(pro) in complex with dual inhibitors, a zinc ion and a Michael acceptor. The complex structure elaborates a unique mechanism of two distinct inhibitors synergizing to inactivate the protease, providing a structural basis to design novel antivirals and suggesting the potential to take advantage of zinc as an adjunct therapy against CoV-associated diseases. Coronaviruses (CoVs) have the largest genome size among all RNA viruses. CoV infection causes various diseases in humans and animals, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). No approved specific drugs or vaccinations are available to treat their infections. Here, we report a novel dual inhibition mechanism targeting CoV main protease (M(pro)) from feline infectious peritonitis virus (FIPV), which leads to lethal systemic granulomatous disease in cats. M(pro), conserved across all CoV genomes, is essential for viral replication and transcription. We demonstrated that zinc ion and a Michael acceptor-based peptidomimetic inhibitor synergistically inactivate FIPV M(pro). We also solved the structure of FIPV M(pro) complexed with two inhibitors, delineating the structural view of a dual inhibition mechanism. Our study provides new insight into the pharmaceutical strategy against CoV M(pro) through using zinc as an adjuvant therapy to enhance the efficacy of an irreversible

  6. Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for beta-lactam acetylation.

    Science.gov (United States)

    He, Hongzhen; Ding, Yi; Bartlam, Mark; Sun, Fei; Le, Yi; Qin, Xincheng; Tang, Hong; Zhang, Rongguang; Joachimiak, Andrzej; Liu, Jinyuan; Zhao, Nanming; Rao, Zihe

    2003-01-31

    Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55A resolution. The binary complex forms a characteristic "V" shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

  7. Crystal Structures of the Pro-Inflammatory Cytokine Interleukin-23 and Its Complex with a High-Affinity Neutralizing Antibody

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Brian M.; Ingram, Richard; Ramanathan, Lata; Reichert, Paul; Le, Hung V.; Madison, Vincent; Orth, Peter (SPRI)

    2009-06-25

    Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2.9 and 1.9 {angstrom}, respectively. The IL-23 structure closely resembles that of IL-12. They share the common p40 subunit, and IL-23 p19 overlaps well with IL-12 p35. Along the hydrophilic heterodimeric interface, fewer charged residues are involved for IL-23 compared with IL-12. The binding site of the Fab is located exclusively on the p19 subunit, and comparison with published cytokine-receptor structures suggests that it overlaps with the IL-23 receptor binding site.

  8. Crystal structures of salicylideneguanylhydrazinium chloride and its copper(II) and cobalt(III) chloride complexes

    International Nuclear Information System (INIS)

    Chumakov, Yu. M.; Tsapkov, V. I.; Bocelli, G.; Antosyak, B. Ya.; Shova, S. G.; Gulea, A. P.

    2006-01-01

    The crystal structures of salicylideneguanylhydrazinium chloride hydrate hemiethanol solvate (I), salicylideneguanylhydrazinium trichloroaquacuprate(II) (II), and bis(salicylideneguanylhydrazino)cobalt(III) chloride trihydrate (III) are determined using X-ray diffraction. The structures of compounds I, II, and III are solved by direct methods and refined using the least-squares procedure in the anisotropic approximation for the non-hydrogen atoms to the final factors R = 0.0597, 0.0212, and 0.0283, respectively. In the structure of compound I, the monoprotonated molecules and chlorine ions linked by hydrogen bonds form layers aligned parallel to the (010) plane. In the structure of compound II, the salicylaldehyde guanylhydrazone cations and polymer chains consisting of trichloroaquacuprate(II) anions are joined by an extended three-dimensional network of hydrogen bonds. In the structure of compound III, the [Co(LH) 2 ] + cations, chloride ions, and molecules of crystallization water are linked together by a similar network

  9. Crystal structures and Moessbauer spectra of spin-crossover iron(III) complexes of quinquedentate ligands

    International Nuclear Information System (INIS)

    Maeda, Yonezo; Noda, Yosuke; Oshio, Hiroki; Takashima, Yoshimasa; Matsumoto, Naohide

    1994-01-01

    Magnetic properties, Moessbauer spectra and crystal structures of spin-crossover iron(III) complexes with a quinquedentate ligand [FeLX]BPh 4 are reported. X and L denote a unidentate ligand and a quinquedentate ligand, respectively. [Fe(mbpN)(im)]BPh 4 shows spin-crossover behavior in an appropriate organic solvent, and [Fe(mbpN)(lut)]BPh 4 , [Fe(bpN)(py)]BPh 4 and [Fe(salten)X]BPh 4 (X = 4me-py or 2me-im) show spin-crossover behavior in a solid and in an organic solvent. It was found that the ligand field strength of salten was stronger than that of mbpN. The rates of spin-state interexchange in the complexes are as fast as the inverse of the lifetime (1 x 10 -7 s) of the Moessbauer nuclear level. The Moessbauer spectroscopic behavior of [Fe(mbpN)(lut)]BPh 4 and [Fe(bpN)(py)]BPh 4 is different to that of [Fe(salten)X]BPh 4 (X = 4me-py or 2me-im). The difference was ascribed to the different geometrical positions of the corresponding anions. (orig.)

  10. Bowl adamanzanes--bicyclic tetraamines: syntheses and crystal structures of complexes with cobalt(III) and chelating coordinated oxo-anions.

    Science.gov (United States)

    Broge, Louise; Søtofte, Inger; Jensen, Kristian; Jensen, Nicolai; Pretzmann, Ulla; Springborg, Johan

    2007-09-14

    Seven cobalt(III) complexes of the macrobicyclic tetraamine ligand [2(4).3(1)]adamanzane ([2(4).3(1)]adz) are reported along with the crystal structure of six of these complexes. The solid state and solution structures are discussed, and a detailed assignment of the NMR spectra of the sulfato complex is provided. Four of the seven complexes contain a chelate coordinating oxo-anion (sulfate, formiate, nitrate, carbonate). Equilibration of these species with the corresponding diaqua complex is generally slow. The rates of equilibration in 5 mol dm(-3) perchloric acid at 25 degrees C have been measured, yielding half lives of 20 min, 10 min and 3 h for the sulfato, formiato and carbonato species respectively. The corresponding reaction for the nitrato complex occurs with a half life of less than 3 min. The concentration acid dissociation constant for the Co([2(4).3(1)]adz)(HCO(3))(2+) ion has been measured to K(a) = 0.33 mol dm(-3) [25 degrees C, I = 2 mol dm(-3)] and K(a) = 0.15 mol dm(-3) [25 degrees C, I = 5 mol dm(-3)]. The propensity for coordination of sulfate was found to be large enough for a quantitative conversion of the carbonato complex to the sulfato complex to occur in 3 mol dm(-3) triflic acid containing a small sulfate contamination. On this basis the decarboxylation in 5 mol dm(-3) triflic acid of the corresponding cobalt(III) carbonato complex of the larger macrobicyclic tetraamine ligand [3(5)]adz was reinvestigated and found to lead to the sulfato complex as well. The difference in exchange rate of the oxo-anion ligands for the cobalt(III) complexes of the two adamanzane ligands is discussed and attributed to fundamental differences in the molecular structure where an inverted configuration of the secondary non-bridged amine groups is seen for the complexes of the larger [3(5)]adz ligand. The high affinity for chelating coordination of oxo-anions for these two cobalt(iii)-adamanzane-moieties is rationalised on basis of the N-Co-N angles. N

  11. The crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with adenosine

    Energy Technology Data Exchange (ETDEWEB)

    Giuseppe, P.O.; Meza, A.N.; Martins, N.H.; Santos, C.R.; Murakami, M.T. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil)

    2012-07-01

    Full text: Purine nucleoside phosphorylases (PNPs) play a key role in the purine-salvage pathway in both prokaryotes and eukaryotes. Its ribosyltransferase activity is of great biotechnological interest due to potential application in the synthesis of nucleoside analogues used in the treatment of antiviral infections and in anticancer chemotherapy. Trimeric PNPs are found mainly in vertebrates and are specific for 6-oxo-purines whereas hexameric PNPs are prevalent in prokaryotes and exhibit a broad range of substrates including 6-oxo and 6-amino purines. BsPNP233, the hexameric PNP from B. subtilis, is able to catalyze the bioconversion of ribavirin, an anti-viral drug, and is relatively thermostable, being a good target for industrial use. Here we report the crystal structures of BsPNP233 in the apo form and in complex with adenosine solved at 2.65 and 1.91 resolution, respectively. The apo and ligand-bound BsPNP233 subunits superposed with an overall r.m.s. deviation of 0.31 for all C{alpha} atoms, which suggests that no major conformational changes occur upon substrate binding. Based on the crystal structure of BsPNP233 in complex with adenosine we have defined the active site residues implicated in binding the ribose (H4{sup *}, R43{sup *}, M64, R87, E178, M179, E180) and the nitrogenous base (S90, C91, G92, S202, V177, F159). These residues are highly conserved among the bacterial hexameric PNPs, suggesting they share the same mode of interaction with the substrates. This work will probably contribute to a better understanding of the molecular basis for the broad substrate specificity of hexameric PNPs and to projects aiming the rational design of PNPs for industrial purposes. (author)

  12. Synthesis, crystal structure, and spectroscopic characterization of two new binuclear complexes of manganese(II) and vanadium(V) with dipicolinate ligands containing 2-aminopyrimidinium as a counter cation

    Czech Academy of Sciences Publication Activity Database

    Tabatabaee, M.; Mahmoodikhah, H.; Ahadiat, G.; Dušek, Michal; Pojarová, Michaela

    2013-01-01

    Roč. 144, č. 5 (2013), s. 621-626 ISSN 0026-9247 R&D Projects: GA ČR(CZ) GAP204/11/0809 Institutional support: RVO:68378271 Keywords : manganese complex * vanadium complex * dipicolinic ligand * crystal structure Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.347, year: 2013

  13. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatecobalt(II

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-01-01

    Full Text Available The structure of the mononuclear title complex, [{(H3CS2C=NC[triple-bond] N}2CoCl2], consists of a CoII atom coordinated in a distorted tetrahedral manner by two Cl− ligands and the terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515 (su? Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.

  14. Characteristic Ligand-Induced Crystal Forms of HIV-1 Protease Complexes: A Novel Discovery of X-Ray Crystallography

    International Nuclear Information System (INIS)

    Olajuyigbe, Folasade M.; Geremia, Silvano

    2009-10-01

    Mixtures of saquinavir (SQV) and ritonavir (RTV) were cocrystallized with HIV-1 protease (PR) in an attempt to compare their relative potencies using a crystallographic approach and factors responsible for the respective crystal forms obtained were examined. The mixture ratio of the SQV/RTV was in the range of 1:1 to 1:50 with increasing concentration of dimethyl sulphoxide (DMSO) used. Two crystal forms of PR complexes were obtained. At concentrations of 0.8 and 1.2 % DMSO using 1:1 and 1:15 ratios of SQV/RTV, the crystal form was monoclinic while increasing the concentration of DMSO to 3.2 and 5.0% using 1:15 and 1:50 ratios of SQV/RTV, the orthorhombic crystal form was obtained. The high resolution X-ray crystal structures of the PR/ inhibitor complexes reveal that crystal forms with respective space groups are dependent on the occupancy of either SQV or RTV in the active site of the PR. The occupancy of either of the PR inhibitors in the active site of PR has interestingly demonstrated unique cooperativity effects in crystallization of protein-ligand complexes. The crystal forms obtained were also related to the concentration of DMSO and ammonium sulphate in crystallization, and storage conditions of purified PR. Surprisingly, the relative occupancies of these inhibitors in the active site suggested a competition between the two inhibitors which were not inhibition constants related. Analysis of the structures in both crystal forms show no difference in DMSO content but at higher concentration of DMSO (3.2 - 5.0%) in the orthorhombic crystal forms, there were protein-sulphate interactions which were absent in the monoclinic forms with lower concentration (0.8 - 1.2%) of DMSO. This work has clearly demonstrated that there is cooperativity in crystallization and the conditions of crystallization influence specific intermolecular contacts in crystal packing (crystal form). (author)

  15. Synthesis and Crystal Structure of a 4,4'-bipyridine Linked Dinuclear Copper(II) Complex Derived from 2-{[2-(2-hydroxyethylamino)ethylimino]methyl}-6-methylphenol.

    Science.gov (United States)

    Zhang, Xiu-Zhen; Gu, Yitong; Li, Yuntong; Liu, Andong; Liu, Fuyao; You, Zhonglu; Zhu, Hai-Liang

    2016-12-01

    A novel 4,4'-bipyridine linked dinuclear copper(II) complex, [Cu2L2(bipy)](NO3)2·bipy (L = 2-[2-(2-hydroxyethylamino) ethylimino]methyl-6-methylphenol; bipy = 4,4'-bipyridine), was prepared and characterized by elemental analyses, IR spectroscopy, and single-crystal X-ray diffraction. The Cu···Cu distance is 11.129(2) Å. The CuII atom is coordinated by one phenolate O, one imine N, and one amine N atoms of a Schiff base ligand, and one N atom of the bridging 4,4'-bipyridine ligand, forming a square planar geometry. In the crystal structure of the complex, the dinuclear copper complex cations are linked by 4,4'-bipyridine molecules through intermolecular O-H···N hydrogen bonds, to form 1D chains running in the [2 0 -1] direction.

  16. A structurally characterized organometallic plutonium(IV) complex

    Energy Technology Data Exchange (ETDEWEB)

    Apostolidis, Christos; Walter, Olaf [European Commission, Joint Research Centre, Directorate G - Nuclear Safety and Security, Karlsruhe (Germany); Vogt, Jochen; Liebing, Phil; Edelmann, Frank T. [Chemisches Institut, Otto-von-Guericke-Universitaet Magdeburg (Germany); Maron, Laurent [Laboratoire de Physique et Chimie des Nanoobjets (LPCNO), Universite de Toulouse/INSA/CNRS (UMR5215), Toulouse (France)

    2017-04-24

    The blood-red plutonocene complex Pu(1,3-COT'')(1,4-COT'') (4; COT''=η{sup 8}-bis(trimethylsilyl)cyclooctatetraenyl) has been synthesized by oxidation of the anionic sandwich complex Li[Pu(1,4-COT''){sub 2}] (3) with anhydrous cobalt(II) chloride. The first crystal structure determination of an organoplutonium(IV) complex revealed an asymmetric sandwich structure for 4 where one COT'' ring is 1,3-substituted while the other retains the original 1,4-substitution pattern. The electronic structure of 4 has been elucidated by a computational study, revealing a probable cause for the unexpected silyl group migration. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. Expression, refolding and crystallization of murine MHC class I H-2Db in complex with human β2-microglobulin

    International Nuclear Information System (INIS)

    Sandalova, Tatyana; Michaëlsson, Jakob; Harris, Robert A.; Ljunggren, Hans-Gustaf; Kärre, Klas; Schneider, Gunter; Achour, Adnane

    2005-01-01

    Mouse MHC class I H-2Db in complex with human β2m and the LCMV-derived peptide gp33 has been produced and crystallized. Resolution of the structure of this complex combined with the structural comparison with the previously solved crystal structure of H-2Db/mβ2m/gp33 should lead to a better understanding of how the β2m subunit affects the overall conformation of MHC complexes as well as the stability of the presented peptides. β 2 -Microglobulin (β 2 m) is non-covalently linked to the major histocompatibility (MHC) class I heavy chain and interacts with CD8 and Ly49 receptors. Murine MHC class I can bind human β 2 m (hβ 2 m) and such hybrid molecules are often used in structural and functional studies. The replacement of mouse β 2 m (mβ 2 m) by hβ 2 m has important functional consequences for MHC class I complex stability and specificity, but the structural basis for this is unknown. To investigate the impact of species-specific β 2 m subunits on MHC class I conformation, murine MHC class I H-2D b in complex with hβ 2 m and the peptide gp33 derived from lymphocytic choriomeningitis virus (LCMV) has been expressed, refolded in vitro and crystallized. Crystals containing two complexes per asymmetric unit and belonging to the space group P2 1 , with unit-cell parameters a = 68.1, b = 65.2, c = 101.9 Å, β = 102.4°, were obtained

  18. Crystal structure of di-( N-methylmorpholine betaine)- L(+)-tartrate

    Science.gov (United States)

    Dega-Szafran, Z.; Dutkiewicz, G.; Kosturkiewicz, Z.; Szafran, M.

    2002-11-01

    The crystal structure of di-( N-methylmorpholine betaine)- L(+)-tartrate has been determined by X-ray diffraction method. Crystals are orthorhombic, space group P2 12 12 1, a=9.580(1), b=12.208(1), c=18.677(1) Å, Z=4, R=0.037. The molecule of L(+)-tartaric acid appears in the extended form with the hydroxyl groups as well as carboxyl groups in anti positions. The molecule is involved in a number of the intra- and intermolecular hydrogen bonds. The COOH groups of the tartaric acid link two non-equivalent N-methylmorpholine betaine molecules by a short, intermolecular O-H⋯O bonds of the lengths 2.456(1) and 2.510(1) Å. The OH groups form two different bifurcated hydrogen bonds, the intramolecular with the CO oxygen atoms (2.641(2) and 2.638(2) Å) and the intermolecular (2.919(2) and 3.084(2) Å) with neighbouring tartaric acid molecules, and link complexes in the zigzag ribbon parallel to the x-axis. The morpholine rings of both betaine molecules are in chair conformation with methyl groups in an axial position and CH 2COO - substituents in an equatorial one. In the crystals and the PM3-optimized structures there is no symmetry, both in the tartrate and N-methylmorpholine betaine moieties. FTIR spectrum confirms the complex structure of the investigated molecule.

  19. Crystal structure and magnetic susceptibility of UOSe single crystals

    International Nuclear Information System (INIS)

    Kaczorowski, D.; Muenster Univ.; Poettgen, R.; Jeitschko, W.; Gajek, Z.; Zygmunt, A.

    1993-01-01

    The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T N =100±2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author)

  20. Crystal structure and magnetic susceptibility of UOSe single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kaczorowski, D. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Poettgen, R.; Jeitschko, W. (Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Gajek, Z.; Zygmunt, A. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research)

    1993-01-01

    The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T[sub N]=100[+-]2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author).

  1. Crystallization and preliminary crystallographic studies of the YafN–YafO complex from Escherichia coli

    International Nuclear Information System (INIS)

    Zhang, Fan; Xing, Li; Teng, Maikun; Li, Xu

    2012-01-01

    The ribosome-dependent mRNA interferase YafO from Escherichia coli belongs to a type II toxin–antitoxin (TA) system and its cognate antitoxin YafN neutralizes cell toxicity by forming a stable YafN–YafO complex. Here, the YafN–YafO complex has been expressed and crystallized. The ribosome-dependent mRNA interferase YafO from Escherichia coli belongs to a type II toxin–antitoxin (TA) system and its cognate antitoxin YafN neutralizes cell toxicity by forming a stable YafN–YafO complex. The YafN–YafO TA system is upregulated by the SOS response (a global response to DNA damage in which the cell cycle is arrested and mutagenesis is induced) and may then inhibit protein synthesis by endoribonuclease activity of YafO with the 50S ribosome subunit. Structural information on the YafN–YafO complex and related complexes would be helpful in order to understand the structural basis of the mechanism of mRNA recognition and cleavage, and the assembly of these complexes. Here, the YafN–YafO complex was expressed and crystallized. Crystals grown by the hanging-drop vapour-diffusion method diffracted to 3.50 Å resolution and belonged to the hexagonal space group P622, with unit-cell parameters a = 86.14, b = 86.14, c = 173.11 Å, α = β = 90, γ = 120°. Both Matthews coefficient analysis and the self-rotation function suggested the presence of one molecule per asymmetric unit in the crystal, with a solvent content of 65.69% (V M = 3.58 Å 3 Da −1 )

  2. Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERα in complex with synthetic ligands

    International Nuclear Information System (INIS)

    Cura, Vincent; Gangloff, Monique; Eiler, Sylvia; Moras, Dino; Ruff, Marc

    2007-01-01

    A new crystallization strategy: the presence of cleaved thioredoxin fusion is critical for crystallization of the estrogen nuclear receptor ligand binding domain in complex with synthetic ligands. This novel technique should be regarded as an interesting alternative for crystallization of difficult proteins. The ligand-binding domain (LBD) of human oestrogen receptor α was produced in Escherichia coli as a cleavable thioredoxin (Trx) fusion in order to improve solubility. Crystallization trials with either cleaved and purified LBD or with the purified fusion protein both failed to produce crystals. In another attempt, Trx was not removed from the LBD after endoproteolytic cleavage and its presence promoted nucleation and subsequent crystal growth, which allowed the structure determination of two different LBD–ligand–coactivator peptide complexes at 2.3 Å resolution. This technique is likely to be applicable to other low-solubility proteins

  3. The Gd14Ag51 structure type and its relation to some complex amalgam structures

    International Nuclear Information System (INIS)

    Tambornino, Frank; Sappl, Jonathan; Hoch, Constantin

    2015-01-01

    Highlights: • The Gd 14 Ag 51 structure type has been revisited on the basis of single crystal diffraction data. • Symmetry analysis from electron density and TEM shows the space group P6/m to be true. • Gd 14 Ag 51 shows good metallic behaviour. • Structure relations to alkali, alkaline-earth and rare-earth metal amalgams can be established. • Complexity values for the RE 14 Ag 51 structure family were calculated. - Abstract: A plethora of binary and ternary intermetallic compounds has been assigned to the Gd 14 Ag 51 structure type, crystallising in the hexagonal system (space group P6/m, a = 1264.30(18) pm, c = 933.58(11) pm for Gd 14 Ag 51 ). Starting in the late 1960s, much work has been invested in the structural elucidation of these crystal structures. However, reliable single crystal data are scarce, and most structure type assignments have been performed merely on the basis of powder data. We have redetermined four representatives of the binary RE 14 Ag 51 structure type (RE = Y, Ce, Gd, Tb) with modern high-precision single crystal X-ray methods. The assignment of the Gd 14 Ag 51 structure type to space group P6/m was additionally verified by careful analysis of high resolution transmission electron micrographs. We emphasise the close relation of the Gd 14 Ag 51 structure type to the structures of some recently described amalgams of similar composition focussing on disorder phenomena and structural complexity. Furthermore, we provide detailed information on synthesis as well as electrical and magnetic properties for Gd 14 Ag 51 , the parent compound of this structure family

  4. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    Beyer, Theresa

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  5. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  6. Crystal structure and spin state of mixed-crystals of iron with zinc and cobalt for the assembled complexes bridged by 1,3-bis(4-pyridyl)propanes

    Energy Technology Data Exchange (ETDEWEB)

    Dote, Haruka [Hiroshima University, Graduate School of Science (Japan); Nakashima, Satoru, E-mail: snaka@hiroshima-u.ac.jp [Hiroshima University, Natural Science Center for Basic Research and Development (Japan)

    2012-03-15

    Mixed crystals of cobalt and zinc were synthesized using 1,3-bis(4-pyridyl)propane (bpp) as bridging ligand and NCS{sup - } as anion. Red crystals and blue crystals were obtained. Powder X-ray diffraction patterns showed that the former is in 2D interpenetrated structure, while the latter has the same structure with Zn(NCS){sub 2}(bpp). Iron ion was introduced both into the red crystals and blue crystals of the mixed crystals of cobalt with zinc. {sup 57}Fe Moessbauer spectrum of the red crystals showed a main doublet of Fe{sup II} high-spin state at 78 K, while the spectrum of blue crystals did not show Fe{sup II} high-spin state at 78 K.

  7. Crystal structure and spin state of mixed-crystals of iron with zinc and cobalt for the assembled complexes bridged by 1,3-bis(4-pyridyl)propanes

    International Nuclear Information System (INIS)

    Dote, Haruka; Nakashima, Satoru

    2012-01-01

    Mixed crystals of cobalt and zinc were synthesized using 1,3–bis(4–pyridyl)propane (bpp) as bridging ligand and NCS  −  as anion. Red crystals and blue crystals were obtained. Powder X-ray diffraction patterns showed that the former is in 2D interpenetrated structure, while the latter has the same structure with Zn(NCS) 2 (bpp). Iron ion was introduced both into the red crystals and blue crystals of the mixed crystals of cobalt with zinc. 57 Fe Mössbauer spectrum of the red crystals showed a main doublet of Fe II high-spin state at 78 K, while the spectrum of blue crystals did not show Fe II high-spin state at 78 K.

  8. Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for {beta}-lactam acetylation.

    Energy Technology Data Exchange (ETDEWEB)

    He, H.; Ding, Y.; Bartlam, M.; Sun, F.; Le, Y.; Qin, X.; Tang, H.; Zhang, R.; Joachimiak, A.; Liu, J.; Zhao, N.; Rao, Z.; Biosciences Division; Tsinghua Univ.; Chinese Academy of Science

    2003-01-31

    Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55 {angstrom} resolution. The binary complex forms a characteristic 'V' shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

  9. Crystal structure of a supramolecular lithium complex of p-tert-butylcalix[4]arene

    Directory of Open Access Journals (Sweden)

    Manabu Yamada

    2018-05-01

    Full Text Available Crystals of a supramolecular lithium complex with a calix[4]arene derivative, namely tetramethanollithium 5,11,17,23-tetra-tert-butyl-25,26,27-trihydroxy-28-oxidocalix[4]arene methanol monosolvate, [Li(CH3OH4](C44H55O4·CH3OH or [Li(CH3OH4]+·(calix[4]arene−]·CH3OH (where calix[4]arene− represents a mono-anion species because of deprotonation of one H atom of the calixarene hydroxy groups, were obtained from p-tert-butylcalix[4]arene reacted with LiH in tetrahydrofuran, followed by recrystallization from methanol. The asymmetric unit comprises one mono-anionic calixarene molecule, one Li+ cation coordinated to four methanol molecules, and one methanol molecule included in the calixarene cavity. The calixarene molecule maintains a cone conformation by intramolecular hydrogen bonding between one phenoxide (–O− and three pendent calixarene hydroxy groups (–OH. The coordinated methanol molecules around the metal cation play a significant role in forming the supramolecular assembly. The crystal structure of this assembly is stabilized by three sets of intermolecular interactions: (i hydrogen bonds involving the –OH and –O− moieties of the calixarene molecules, the –OH groups of the coordinated methanol molecules, and the –OH group of the methanol molecule included in the calixarene cavity; (ii C—H...π interactions between the calixarene molecules and/or the coordinated methanol molecules; (iii O—H...π interactions between the calixarene molecule and the included methanol molecule.

  10. Structural aspects of inotropic bipyridine binding. Crystal structure determination to 1.9 A of the human serum transthyretin-milrinone complex.

    Science.gov (United States)

    Wojtczak, A; Luft, J R; Cody, V

    1993-03-25

    The crystal structure of human transthyretin (TTR) complexed with milrinone (2-methyl-5-cyano-3,4'-bipyridin-6(1H)-one), a positive inotropic cardiac agent, has been refined to R = 17.4% for 8-1.9-A resolution data. This report provides the first detailed description of protein interactions for an inotropic bipyridine agent which is an effective thyroid hormone binding competitor to transthyretin. Milrinone is bound along the 2-fold axis in the binding site with its substituted pyridone ring located deep within the channel of the two identical binding domains of the TTR tetramer. In this orientation the 5-cyano group occupies the same site as the 3'-iodine in the TTR complex with 3,3'-diiodothyronine (Wojtczak, A., Luft, J., and Cody, V. (1992) J. Biol. Chem. 267, 353-357), which is 3.5 A deeper in the channel than thyroxine (Blake, C. C. F., and Oately, S. J., (1977) Nature 268, 115-120). These structural results confirm computer modeling studies of milrinone structural homology with thyroxine and its TTR binding interactions and explain the effectiveness of milrinone competition for thyroxine binding to TTR. To understand the weaker binding affinity of the parent inotropic drug, amrinone (5-amino-3,4'-bipyridin-6(1H)-one), modeling studies of its TTR binding were carried out which indicate that the 5-amino group cannot participate in strong interactions with TTR and the lack of the 2-methyl further weakens amrinone binding.

  11. Crystallization and preliminary crystallographic analysis of the measles virus hemagglutinin in complex with the CD46 receptor

    International Nuclear Information System (INIS)

    Santiago, César; Gutiérrez-Rodríguez, Angel; Tucker, Paul A.; Stehle, Thilo; Casasnovas, José M.

    2009-01-01

    A complex of the measles virus hemagglutinin and the CD46 receptor representing the initial step of the cell infection has been crystallized. The measles virus (MV) hemagglutinin (MV-H) mediates the attachment of MV particles to cell-surface receptors for entry into host cells. MV uses two receptors for attachment to host cells: the complement-control protein CD46 and the signalling lymphocyte activation molecule (SLAM). The MV-H glycoprotein from an Edmonston MV variant and the MV-binding fragment of the CD46 receptor were overproduced in mammalian cells and used to crystallize an MV-H–CD46 complex. Well diffracting crystals containing two complexes in the asymmetric unit were obtained and the structure of the complex was solved by the molecular-replacement method

  12. Synthesis and Crystal Structure of a Three—dimensionla Manganese(Ⅱ)Complex COnstructed via Covalent and Hydrogen Bonds

    Institute of Scientific and Technical Information of China (English)

    WANGRui-Hu; ChenLi-Hua; 等

    2003-01-01

    The assembly of 1,4-benzenedicarboxylic acid (H2bdc),4,4′-bipyridine (4,4′-bipy),trimethyltin chloride and MnBr2.4H2O in hydrothermal conditions gave rise to a hydrogen-bonded three-dimensional complex {Mn(4,4′-bipy).4H2O](bdc}nwhich has been characterized by single-crystal X-ray diffraction.The complex crystallizes in the monoclinic system,space group,P2/n with a=7.0001(2),b=11.5540(3),c=11.4192(1)°↑A,β=101.754(2)°,V=904.21(4)°↑A3,Z=2,C18H20MnN2O8,Mr=447.30,Dc=1.643 g/cm3,F(000)=462 and μ(Mokα)=0.783mm1,The final R and wR are 0.0499 and 0.1301,respectively for 1335 observed reflctions with I≥2σ(I).The Mn(Ⅱ)is six-coordinated in a distorted octahedral geometry,4,4′-Bipyridine in a μ-bridge mode links [Mn(H2O)4]2+ into a linear cation chain.bdc acts as a counter anion and links the linear chains into a three-dimensional structure through hydrogen bonds.

  13. Production, crystallization and preliminary X-ray diffraction of the Gαs α-helical domain in complex with a nanobody.

    Science.gov (United States)

    Triest, Sarah; Wohlkönig, Alexandre; Pardon, Els; Steyaert, Jan

    2014-11-01

    GPCR-G-protein complexes are one of the most important components of cell-signalling cascades. Extracellular signals are sensed by membrane-associated G-protein-coupled receptors (GPCRs) and transduced via G proteins towards intracellular effector molecules. Structural studies of these transient complexes are crucial to understand the molecular details of these interactions. Although a nucleotide-free GPCR-G-protein complex is stable, it is not an ideal sample for crystallization owing to the intrinsic mobility of the Gαs α-helical domain (AHD). To stabilize GPCR-G-protein complexes in a nucleotide-free form, nanobodies were selected that target the flexible GαsAHD. One of these nanobodies, CA9177, was co-crystallized with the GαsAHD. Initial crystals were obtained using the sitting-drop method in a sparse-matrix screen and further optimized. The crystals diffracted to 1.59 Å resolution and belonged to the monoclinic space group P2₁, with unit-cell parameters a=44.07, b=52.55, c=52.66 Å, α=90.00, β=107.89, γ=90.00°. The structure of this specific nanobody reveals its binding epitope on GαsAHD and will help to determine whether this nanobody could be used as crystallization chaperone for GPCR-G-protein complexes.

  14. Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA

    International Nuclear Information System (INIS)

    Vassylyeva, Marina N.; Svetlov, Vladimir; Klyuyev, Sergiy; Devedjiev, Yancho D.; Artsimovitch, Irina; Vassylyev, Dmitry G.

    2006-01-01

    The E. coli transcriptional regulator RfaH was cloned, expressed, purified and crystallized and the complex of RfaH with its target DNA oligonucleotide was cocrystallized. Complete diffraction data sets were collected for the apo protein and its nucleic acid complex at 2.4 and at 1.6 Å resolution, respectively. The bacterial transcriptional factor and virulence regulator RfaH binds to rapidly moving transcription elongation complexes through specific interactions with the exposed segment of the non-template DNA strand. To elucidate this unusual mechanism of recruitment, determination of the three-dimensional structure of RfaH and its complex with DNA was initiated. To this end, the Escherichia coli rfaH gene was cloned and expressed. The purified protein was crystallized by the sitting-drop vapor-diffusion technique. The space group was P6 1 22 or P6 5 22, with unit-cell parameters a = b = 45.46, c = 599.93 Å. A complex of RfaH and a nine-nucleotide oligodeoxyribonucleotide was crystallized by the same technique, but under different crystallization conditions, yielding crystals that belonged to space group P1 (unit-cell parameters a = 36.79, b = 44.01, c = 62.37 Å, α = 80.62, β = 75.37, γ = 75.41°). Complete diffraction data sets were collected for RfaH and its complex with DNA at 2.4 and 1.6 Å resolution, respectively. Crystals of selenomethionine-labeled proteins in both crystal forms were obtained by cross-microseeding using the native microcrystals. The structure determination of RfaH and its complex with DNA is in progress

  15. Copper-based metal coordination complexes with Voriconazole ligand: Syntheses, structures and antimicrobial properties

    Science.gov (United States)

    Zhao, Yan-Ming; Tang, Gui-Mei; Wang, Yong-Tao; Cui, Yue-Zhi; Ng, Seik Weng

    2018-03-01

    Three new chiral metal coordination complexes, namely, [Cu(FZ)2(CH3COO)2(H2O)]·2H2O (1), [Cu(FZ)2(NO3)2] (2), and [Cu2(FZ)2 (H2O)8](SO4)2·4H2O (3) [FZ = (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoro-4-pyrimidiny)-1-(1H-1,2,4-triazol-1-yl)-2-butanol) (Voriconazole)] have been obtained by the reaction of Cu(II) salts and the free ligand FZ at room temperature. Complexes 1-3 were structurally characterized by X-ray single-crystal diffraction, IR, UV-vis, powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). Complex 1 crystallizes in the chiral space group C2, which exhibits a mono-nuclear structure. Both complexes 2 and 3 display a one-dimensional (1D) tape structure, which crystallize in chiral space group P21212 and P212121, respectively. Among these complexes, there exist a variety of hydrogen bonds and stacking interactions, through which a three-dimensional supramolecular architecture will be generated. Compared with the standard (Voriconazole), these Cu-based complexes show the more potent inhibiting efficiency against the species of Candida and Aspergillus. Moreover, among these complexes, complex 1 shows the most excellent efficiency.

  16. Crystal structure of mixed ligand compound [HgPhen{(C2H5)2NCS2}2] and character of intermolecular interaction in the structures of [MPhen{(C2H5)2NCS2}2] (M = Zn, Cd, Hg) complexes

    International Nuclear Information System (INIS)

    Klevtsova, R.F.; Glinskaya, L.A.; Zemskova, S.M.; Larionov, S.V.

    2002-01-01

    Monocrystals of mixed ligand complex [HgPhen(Et 2 NCS 2 ) 2 ] (Phen = 1, 10-phenanthroline) have been prepared and by the method of X-ray diffraction its crystal structure has been determined. The structure of mercury complex has been compared with structures of previously studied cadmium and zinc complexes similar in composition. The character of interaction between molecules of cadmium, zinc, mercury mixed ligand complexes and ways of their packing have been considered. It is shown that the structure of the complexes presents a molecular group assembled from two monomeric compounds at the expense of interaction between heterocyclic ligands contained in the mixed ligand complexes [ru

  17. Crystal structure of product-bound complex of UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

    Energy Technology Data Exchange (ETDEWEB)

    Pampa, K.J., E-mail: sagarikakj@gmail.com [Department of Studies in Microbiology, University of Mysore, Mysore 570 006 (India); Lokanath, N.K. [Department of Studies in Physics, University of Mysore, Mysore 570 006 (India); Girish, T.U. [Department of General Surgery, JSS Medical College and Hospital, JSS University, Mysore 570 015 (India); Kunishima, N. [Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148 (Japan); Rai, V.R. [Department of Studies in Microbiology, University of Mysore, Mysore 570 006 (India)

    2014-10-24

    Highlights: • Determined the structure of UDP-D-ManNAcADH to a resolution of 1.55 Å. • First complex structure of PhUDP-D-ManNAcADH with UDP-D-ManMAcA. • The monomeric structure consists of three distinct domains. • Cys258 acting as catalytic nucleophilic and Lys204 acts as acid/base catalyst. • Oligomeric state plays an important role for the catalytic function. - Abstract: UDP-N-acetyl-D-mannosamine dehydrogenase (UDP-D-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-D-mannosamine (UDP-D-ManNAc) to Uridine-diphospho-N-acetyl-D-mannosaminuronic acid (UDP-D-ManNAcA) through twofold oxidation of NAD{sup +}. In order to reveal the structural features of the Pyrococcus horikoshii UDP-D-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55 Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-D-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.

  18. Synthesis and crystal structure of the rhodium(I) cyclooctadiene complex with bis(3-tert-butylimidazol-2-ylidene)borate ligand

    Energy Technology Data Exchange (ETDEWEB)

    Chen, F.; Shao, K.-J.; Xiao, Y.-C.; Pu, X.-J.; Zhu, B., E-mail: zhubao-999@126.com [Affiliated Wuxi Peoples Hospital, Department of Nuclear Medicine, Nanjing Medical University (China); Jiang, M.-J., E-mail: jmj16888@126.com [Affiliated Wuxi Peoples Hospital, Department of Clinical Laboratory Science, Nanjing Medical University (China)

    2015-12-15

    The rhodium(I) cyclooctadiene complex with the bis(3-tert-butylimidazol-2-ylidene)borate ligand [H{sub 2}B(Im{sup t}Bu){sup 2}]Rh(COD) C{sup 22}H{sup 36}BN{sup 4}Rh, has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal center, which is coordinated by the bidentate H{sup 2}B(Im{sup t}Bu){sub 2} and one cyclooctadiene group. The Rh–C{sub carbene} bond lengths are 2.043(4) and 2.074(4) Å, and the bond angle C–Rh1–C is 82.59°. The dihedral angle between two imidazol-2-ylidene rings is 67.30°.

  19. Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

    Science.gov (United States)

    Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

    2016-01-01

    Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

  20. Crystal nucleation in simple and complex fluids.

    Science.gov (United States)

    Oxtoby, David W

    2003-03-15

    The application of density-functional methods from statistical mechanics to the nucleation of crystals from the melt is described. Simple fluids such as metals, with sizes comparable with the range of their attractive forces, are compared with complex fluids such as colloidal suspensions and proteins dissolved in solution. A different mechanism for crystal nucleation is proposed in the latter case, in which density (concentration) changes before periodic crystalline order appears. This leads to a theoretical foundation for empirical observations on the 'crystallization window' in protein crystallization. Comparisons are made with the results of computer simulation via molecular dynamics.

  1. Potassium and magnesium succinatouranilates – Synthesis and crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Novikov, S.A., E-mail: serg.alex.novikov@gmail.com [Samara National Research University, 443086 Samara (Russian Federation); Grigoriev, M.S. [Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 119071 Moscow (Russian Federation); Serezhkina, L.B.; Serezhkin, V.N. [Samara National Research University, 443086 Samara (Russian Federation)

    2017-04-15

    Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}] [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), where C{sub 4}H{sub 4}O{sub 4}{sup 2-} is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} with the same A{sub 2}Q{sup 02}{sub 3} crystallochemical formula (A=UO{sub 2}{sup 2+}, Q{sup 02}=C{sub 4}O{sub 4}H{sub 4}{sup 2-}), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ions is one of the factors, which affects the structure of [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A{sub 2}Q{sup 02}{sub 3} crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality. - Graphical abstract: Crystal structures of two new uranium(VI) coordination polymers with succinate linkers, namely K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), were determined by single-crystal XRD. Crystals of studied compounds are based on 2D or 1D structural units with the same composition and crystallochemical formula. Topological isomerism in A{sub 2}Q{sup 02}{sub 3} crystallochemical group and conformations of succinate anions in uranyl complexes are under discussion. - Highlights: • Two new uranium coordination polymers were synthesized. • Their structural units have the same composition and crystallochemical formula. • In spite the same composition and CCF dimensionality of units is different. • Structural features of uranyl CPs

  2. Synthesis, characterization and crystal structure determination of a new Zn(II Schiff base complex derived from condensation of a new asymmetrical tripodal amine, 3-((4-aminobutyl(pyridin-2-ylmethylaminopropan-1-ol and 2-hydroxy-3-methoxybenzaldehyde

    Directory of Open Access Journals (Sweden)

    Majid Rezaeivala

    2017-05-01

    Full Text Available A new tripodal amine, 3-((4-aminobutyl(pyridin-2-ylmethylaminopropan-1-ol (HL has been prepared. This has been used to synthesize a new Schiff base complex by template condensation with 2-hydroxy-3-methoxybenzaldehyde in the presence of Zn(II metal ion in methanol. The complex has been characterized using spectroscopic methods and the crystal structure of [ZnL]BF4, L:3-((4-aminobutyl(pyridin-2-ylmethylaminopropan-1-ol was confirmed by single crystal X-ray diffraction studies. Single crystal X-ray structure analysis showed that in the mononuclear Zn(II complex, [ZnL]BF4 the Zn(II ion is in a distorted square pyramidal environment.

  3. Crystal structures of unsymmetrically mixed β-pyrrole substituted ...

    Indian Academy of Sciences (India)

    NiTPP(Ph)3(CN)5, 3 complex was synthesized and its solvated structure was examined by crystallography. ... sive interactions among the peripheral substituents.28,29 ... 1H NMR spectra of porphyrins were. 1047 ... Single crystals of MTPP(Ph)3Cl5 (M = 2H and Ni(II)) .... by ∼0.3–0.6ppm but β-pyrrole phenyls do not show.

  4. Synthesis, crystal structures, and characterization of double complex salts [Au(en)2][Rh(NO2)6]·2H2O and [Au(en)2][Rh(NO2)6

    Science.gov (United States)

    Plyusnin, Pavel E.; Makotchenko, Evgenia V.; Shubin, Yury V.; Baidina, Iraida A.; Korolkov, Ilya V.; Sheludyakova, Liliya A.; Korenev, Sergey V.

    2015-11-01

    Double complex salts of rhodium(III) and gold(III) of the composition [Au(en)2][Rh(NO2)6]·2H2O (1) and [Au(en)2][Rh(NO2)6] (2) have been prepared. Crystal structures of the compounds have been determined by single crystal X-ray diffraction. The compounds have been characterized by PXRD, IR, far-IR, CHN and DTA. The complexes have a layered structures. The presence of water in 1 makes the structure of the hydrated DCS less dense as compared to the anhydrous one. The environment of the cation and the anion in the two structures is the same, oxygen atoms of the nitro groups are involved in hydrogen bonds N-H⋯O, N⋯O distances being approximately the same. The structures of 1 and 2 are notable in having shortened contacts between the gold atoms and the oxygen atoms of the nitro groups of the neighboring complex anions. The thermal behavior of the complexes in a hydrogen atmosphere was investigated. The final product of thermolysis prepared at the temperature 600°C is a two-phase mixture of pure metallic gold and the solid solution Rh0.93Au0.07.

  5. Synthesis, crystal structures, spectral, thermal and antimicrobial properties of new Zn(II) 5-iodo- and 5-bromosalicylates

    Science.gov (United States)

    Košická, Petra; Győryová, Katarína; Smolko, Lukáš; Gyepes, Róbert; Hudecová, Daniela

    2018-03-01

    Two new analogous zinc(II) complexes containing 5-iodo- and 5-bromosalicylate ligands, respectively, were prepared in single-crystal form and characterized by IR spectroscopy, thermal analysis and elemental analysis. The solid-state structures of prepared complexes were determined by single crystal X-ray crystallography. Both complexes are isostructural and their crystal structures composed of neutral molecules [Zn(5-Xsal)2(H2O)2] (where X = Br, I, sal = salicylato). Central Zn(II) atom is in both complexes coordinated by six oxygen atoms, four of which are from two chelate bonded 5-halosalicylates and remaining two from coordinated water molecules. The found chelate binding mode is in line with the Δ values calculated from IR spectral data. Antimicrobial activity of prepared complexes was studied against selected bacteria, yeast and filamentous fungi. Obtained results indicate that 5-iodosalicylate complex is more antimicrobially active than its 5-bromo substituted analogue.

  6. Crystal structure of the formal 20 electron zirconocene pentafulvene complex Cp2Zr(η5,η1-adamantylidenepentafulvene:toluene:n-hexane = 1:0.125:0.125

    Directory of Open Access Journals (Sweden)

    Malte Fischer

    2017-12-01

    Full Text Available The crystal structure of a solvated zirconocene pentafulvene complex with a bulky adamantylidene substitution pattern, namely (η5,η1-adamantylidenepentafulvenebis(η5-cyclopentadienylzirconium(IV–toluene–n-hexane (8/1/1, [Zr(C15H18(C5H52]·0.125C7H8·0.125C6H14, is reported. Reducing zirconocene dichloride with magnesium results in the formation of a low-valent zirconocene reagent that reacts readily with adamantylidenepentafulvene to give the aforementioned complex. Single crystal X-ray diffraction proves the dianion-like η5:η1 binding mode of the fulvene ligand to the central ZrIV atom. The asymmetric unit contains four independent molecules of [η5:η1-adamantylidenepentafulvene]bis[(η5-cyclopentadienyl]zirconium(IV, together with half a molecule of toluene disordered with half a molecule of n-hexane (the solvent molecules have no direct influence on the complex. In each of the four complex molecules, the central ZrIV atom has a distorted tetrahedral coordination environment. The measured crystal consisted of two domains with a refined ratio of 0.77:0.23.

  7. Crystal structure of importin-{alpha} complexed with a classic nuclear localization sequence obtained by oriented peptide library screening

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, A.A.S.; Fontes, M.R.M. [UNESP, Universidade Estadual Paulista, Botucatu, SP (Brazil); Yang, S.N.Y. [University of Melbourne, Melbourne (Australia); Harris, J.M. [Queensland University of Technology, Brisbane (Australia); Jans, D.A. [Monash University, Clayton (Australia); Kobe, B. [University of Queensland, Brisbane, QU (Australia)

    2012-07-01

    Full text: Importin-{alpha} (Imp{alpha}) plays a role in the classical nuclear import pathway, binding to cargo proteins with activities in the nucleus. Different Imp{alpha} paralogs responsible for specific cargos can be found in a single organism. The cargos contain nuclear localization sequences (NLSs), which are characterized by one or two clusters of basic amino acids (monopartite and bipartite NLSs, respectively). In this work we present the crystal structure of Imp{alpha} from M. musculus (residues 70-529, lacking the auto inhibitory domain) bound to a NLS peptide (pepTM). The peptide corresponds to the optimal sequence obtained by an oriented peptide library experiment designed to probe the specificity of the major NLS binding site. The peptide library used five degenerate positions and identified the sequence KKKRR as the optimal sequence for binding to this site for mouse Imp{alpha} (70-529). The protein was obtained using an E. coli expression system and purified by affinity chromatography followed by an ion exchange chromatography. A single crystal of Imp{alpha} -pepTM complex was grown by the hanging drop method. The data were collected using the Synchrotron Radiation Source LNLS, Brazil and processed to 2.3. Molecular replacement techniques were used to determine the crystal structure. Electron density corresponding to the peptide was present in both major and minor binding sites The peptide is bound to Imp{alpha} similar as the simian virus 40 (SV40) large tumour (T)-antigen NLS. Binding assays confirmed that the peptide bound to Imp{alpha} with low nM affinities. This is the first time that structural information has been linked to an oriented peptide library screening approach for importin-{alpha}; the results will contribute to understanding of the sequence determinants of classical NLSs, and may help identify as yet unidentified classical NLSs in novel proteins. (author)

  8. GPCR crystal structures: Medicinal chemistry in the pocket.

    Science.gov (United States)

    Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Löber, Stefan

    2015-07-15

    Recent breakthroughs in GPCR structural biology have significantly increased our understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystallized in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand binding pockets in GPCRs. In this review, we summarise the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity or efficacy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Coordination chemistry and bioactivity of Ni2+, Cu2+, and Zn2+ complexes containing a bidentate NS ligand, β-N-phenyldithiocarbazic acid, and the crystal structure of β-hydroxy-β-phenylmethylene α-phenylimine

    International Nuclear Information System (INIS)

    Tarafder, M.T.H.; Ahmed Faizal Shamsuddin; Grouse, Karen A.; Yamin, B.M.; Ali, A.M.; Fun, H.-K.

    2003-07-01

    A bidentate ligand (PhDTCH) with NS donor sequence was prepared from the reaction between carbon disulfide and phenylhydrazine in ethanol. Complexes of this ligand with Ni(II), Cu(II) and Zn(II) were synthesized and characterized by elemental analyses, and various physicochemical techniques. The metal complexes were all four coordinated. In an attempt to resolve the crystal structure of PhDTCH, an ethanolic solution, after leaving for a few days gave bright crystals of PhD6, β-hydroxy-β-phenylmethylene α-phenylimine, the crystal structure of which has been resolved. The crystal packing indicated that it is monoclinic with a space group of P21/n. All of the compounds were tested against different bacteria and fungi, and also against leukemic cell lines. All of the compounds showed weak biological properties compared to standard drugs. (author)

  10. Synthesis, crystal structure and photoluminescence study of green light emitting bis(1[(4-butylphenylimino]methyl naphthalen-2-ol Ni(II complex

    Directory of Open Access Journals (Sweden)

    M. Srinivas

    2016-09-01

    Full Text Available Synthetically feasible and cost effective Ni(II complex phosphor (4 as green organic light emitting diode (OLED was prepared by using Schiff base 1-[(4-butylphenylimino]methyl naphthalen-2-ol (3. The single crystals of Ni(II complex were grown from chloroform and hexane (1:1 v/v solution. The green crystals of the complex were characterized by using single crystal XRD studies and were evaluated for their photophysical properties. From the Diffused Reflectance Spectrum of the complex, the measured band gap energy was found to be 1.83 eV and the PL spectrum of the complex showed emission peak at 519 nm. The excitation peaks at 519 nm were appeared at 394 nm and 465 nm. The Commission Internationale De L'Eclairage (CIE chromaticity diagram indicated that, the complex exhibit green color. Hence, Ni(II complex (4 could be a promising green OLED for developing strong electroluminescent materials for flat panel display applications.

  11. Synthesis, characterization, and crystal structures of diruthenium complexes containing bridging salicylato ligands

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Mingxuan; Yau, Chun Huan; Hu, Yuxin; Tan, Yong Leng Kelvin [Hwa Chong Institution (Singapore); Li, Yingzhou; Ganguly, Rakesh; Leong, Weng Kee [Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore)

    2017-08-03

    The thermal reaction of Ru{sub 3}(CO){sub 12} (1) with salicylic acid, in the presence of triphenylphosphine, pyridine, or dimethylsulfoxide, afforded the dinuclear complexes Ru{sub 2}(CO){sub 4}(μ-O{sub 2}CC{sub 6}H{sub 4}OH){sub 2}L{sub 2} (2) [L = PPh{sub 3} (2a). C{sub 5}H{sub 5}N (2b); (CH{sub 3}){sub 2}SO (2c)]. Complex 2b was further reacted with the aromatic dimmines 2,2'-dipyridine or 1,10-phenanthroline to give the cationic diruthenium complexes [Ru{sub 2}(CO){sub 2}(μ-CO){sub 2}(μ-O{sub 2}CC{sub 6}H{sub 4}OH)(N intersection N){sub 2}]{sup +} (3) [(N intersection N) = 2,2'-dipyridine (3a); 1,10-phenanthroline (3b)], which were isolated as their tetraphenylborate salts. All five novel complexes were characterized spectroscopically and analytically. For 2a-2b and 3a-3b, single-crystal X-ray diffraction studies were also carried out. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Synthesis, Crystal Structure, Gas Absorption, and Separation Properties of a Novel Complex Based on Pr and a Three-Connected Ligand

    Directory of Open Access Journals (Sweden)

    Jie Sun

    2017-12-01

    Full Text Available A novel Pr complex, constructed from a rigid three-connected H3TMTA and praseodymium(III ion, has been synthesized in a mixed solvent system and characterized by X-ray single crystal diffraction, infrared spectroscopy, a thermogravimetric analysis, an element analysis, and powder X-ray diffraction, which reveals that complex 1 crystallizes in a three-dimensional porous framework. Moreover, the thermal stabilities and the fluorescent and gas adsorption and separation properties of complex 1 were investigated systematically.

  13. Synthesis, characterization and crystal structure of a 2-(diethylaminomethylindole ligated dimethylaluminium complex

    Directory of Open Access Journals (Sweden)

    Logan E. Shephard

    2015-10-01

    Full Text Available The title compound, [Al(CH32(C13H17N2] (systematic name; {2-[(diethylaminomethyl]indol-1-yl-κ2N,N′}dimethylaluminium, was prepared by methane elimination from the reaction of 2-(diethylaminomethylindole and trimethylaluminium. The complex crystallizes readily from a concentrated toluene solution in high yield. The asymmetric unit contains two crystallographically independent molecules. Each molecule has a four-coordinate aluminium atom that has pseudo-tetrahedral geometry. C—H...π interactions link the independent molecules into chains extending along the b-axis direction.

  14. Two-dimensional layer architecture assembled by Keggin polyoxotungstate, Cu(II)-EDTA complex and sodium linker: Synthesis, crystal structures, and magnetic properties

    International Nuclear Information System (INIS)

    Liu Hong; Xu Lin; Gao Guanggang; Li Fengyan; Yang Yanyan; Li Zhikui; Sun Yu

    2007-01-01

    Reaction of Keggin polyoxotungstate with copper(II)-EDTA (EDTA=ethylenediamine tetraacetate) complex under mild conditions led to the formation of hybrid inorganic-organic compounds Na 4 (OH)[(Cu 2 EDTA)PW 12 O 40 ].17H 2 O (1) and Na 4 [(Cu 2 EDTA)SiW 12 O 40 ].19H 2 O (2). The single-crystal X-ray diffraction analyses reveal their two structural features: (1) one-dimensional chain structure consisting of Keggin polyoxotungstate and copper(II)-EDTA complex; (2) Two-dimensional layer architecture assembled by the one-dimensional chain structure and sodium linker. The results of magnetic measurements in the temperature range 300-2 K indicated the existence of ferromagnetic exchange interactions between the Cu II ions for both compounds. In addition, TGA analysis, IR spectra, and electrochemical properties were also investigated to well characterize these two compounds. - Graphical abstract: Two new polyoxometalate-based hybrids, Na 4 (OH)[Cu 2 (EDTA)PW 12 O 40 ].17H 2 O (1) and Na 4 [Cu 2 (EDTA)SiW 12 O 40 ].19H 2 O (2), have been synthesized and structurally characterized, which consist of one-dimensional chain structure assembled by Keggin polyoxotungstate and copper(II)-EDTA complex. The chains are further connected to form two-dimensional layer architecture assembled by the one-dimensional chain structure and sodium linker

  15. The crystal structure of the secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A

    Energy Technology Data Exchange (ETDEWEB)

    Dostál, Ji& #345; í; Brynda, Ji& #345; í; Hrušková-Heidingsfeldová, Olga; Sieglová, Irena; Pichová, Iva; & #344; ezá& #269; ová, Pavlína; (ASCR-ICP)

    2010-09-01

    Opportunistic pathogens of the genus Candida cause infections representing a major threat to long-term survival of immunocompromised patients. Virulence of the Candida pathogens is enhanced by production of extracellular proteolytic enzymes and secreted aspartic proteases (Saps) are therefore studied as potential virulence factors and possible targets for therapeutic drug design. Candida parapsilosis is less invasive than C. albicans, however, it is one of the leading causative agents of yeast infections. We report three-dimensional crystal structure of Sapp1p from C. parapsilosis in complex with pepstatin A, the classical inhibitor of aspartic proteases. The structure of Sapp1p was determined from protein isolated from its natural source and represents the first structure of Sap from C. parapsilosis. Overall fold and topology of Sapp1p is very similar to the archetypic fold of monomeric aspartic protease family and known structures of Sap isoenzymes from C. albicans and Sapt1p from C. tropicalis. Structural comparison revealed noticeable differences in the structure of loops surrounding the active site. This resulted in differential character, shape, and size of the substrate binding site explaining divergent substrate specificities and inhibitor affinities. Determination of structures of Sap isoenzymes from various species might contribute to the development of new Sap-specific inhibitors.

  16. Routine phasing of coiled-coil protein crystal structures with AMPLE

    Directory of Open Access Journals (Sweden)

    Jens M. H. Thomas

    2015-03-01

    Full Text Available Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

  17. Expression, purification, crystallization and structure of human adipocyte lipid-binding protein (aP2)

    International Nuclear Information System (INIS)

    Marr, Eric; Tardie, Mark; Carty, Maynard; Brown Phillips, Tracy; Wang, Ing-Kae; Soeller, Walt; Qiu, Xiayang; Karam, George

    2006-01-01

    The crystal structure of human adipocyte lipid-binding protein (aP2) with a bound palmitate is reported at 1.5 Å resolution. Human adipocyte lipid-binding protein (aP2) belongs to a family of intracellular lipid-binding proteins involved in the transport and storage of lipids. Here, the crystal structure of human aP2 with a bound palmitate is described at 1.5 Å resolution. Unlike the known crystal structure of murine aP2 in complex with palmitate, this structure shows that the fatty acid is in a folded conformation and that the loop containing Phe57 acts as a lid to regulate ligand binding by excluding solvent exposure to the central binding cavity

  18. Synthesis, crystal structure and computational chemistry research of a Zinc(II complex: [Zn(Pt(Biim2

    Directory of Open Access Journals (Sweden)

    Teng Fei

    2012-01-01

    Full Text Available The title metal-organic coordination complex [Zn(pt(Biim2] (pt=phthalic acid, benzene-1,2-dicarboxylate, Biim=2,2'-biimidazole 1 has been obtained by using hydrothermal synthesis and characterized by single-crystal X-ray diffraction. The complex crystallizes in monoclinic, space group P21/n with a = 8.5466(15 Å, b = 11.760(2 Å, c = 20.829(4 Å, β = 95.56(2º, V = 2083.5(6 Å3, Mr =497.78, Dc = 1.587 g/cm3, μ(MoKα = 1.226 mm−1, F(000 = 1016, Z = 4, the final R = 0.0564 and wR = 0.1851 for 3656 observed reflections (I > 2σ(I. The elemental analysis, IR, TG and the theoretical calculation were also investigated.

  19. Metal Complexes of New Bioactive Pyrazolone Phenylhydrazones; Crystal Structure of 4-Acetyl-3-methyl-1-phenyl-2-pyrazoline-5-one phenylhydrazone Ampp-Ph

    Directory of Open Access Journals (Sweden)

    Omoruyi G. Idemudia

    2016-05-01

    Full Text Available The condensation reaction of phenylhydrazine and dinitrophenylhydrazine with 4-acetyl and 4-benzoyl pyrazolone precipitated air-stable acetyldinitrophenylhydrazone Ampp-Dh, benzoylphenylhydrazone Bmpp-Ph and benzoyldinitrophenylhydrazone Bmpp-Dh in their keto imine form; a study inspired by the burning interest for the development of new bioactive materials with novel properties that may become alternative therapeutic agents. Elemental analysis, FTIR, 1H, and 13C NMR, and mass spectroscopy have been used to justify their proposed chemical structures, which were in agreement with the single crystal structure of Bmpp-Dh earlier reported according to X-ray crystallography. The single crystal structure of 4-acetyl-3-methyl-1-phenyl--pyrazoline-5-one phenylhydrazone Ampp-Ph, which crystallizes in a triclinic crystal system with a P-1 (No. 2 space group is presented. Octahedral Mn(II, Ni(II, Co(II, and Cu(II complexes of these respective ligands with two molecules each of the bidentate Schiff base, coordinating to the metal ion through the azomethine nitrogen C=N and the keto oxygen C=O, which were afforded by the reaction of aqueous solutions of the corresponding metal salts with the ligands are also reported. Their identity and proposed structures were according to elemental analysis, FTIR spectroscopy, UV-VIS spectrophotometry (electronic spectra and Bohr magnetic moments, as well as thermogravimetric analysis (TGA results. A look at the antibacterial and antioxidant activities of synthesized compounds using the methods of the disc diffusion against some selected bacterial isolates and 1,1-diphenyl-2-picryl-hydrazil (DPPH respectively, showed biological activities in relation to employed standard medicinal drugs.

  20. Nickel(II) and copper(II) complexes of N,N-dialkyl-N‧-3-chlorobenzoylthiourea: Synthesis, characterization, crystal structures, Hirshfeld surfaces and antimicrobial activity

    Science.gov (United States)

    Binzet, Gun; Gumus, Ilkay; Dogen, Aylin; Flörke, Ulrich; Kulcu, Nevzat; Arslan, Hakan

    2018-06-01

    We synthesized four new N,N-dialkyl-N‧-3-chlorobenzoylthiourea ligands (Alkyl: Dimethyl, diethyl, di-n-propyl and di-n-butyl) and their metal complexes with copper and nickel atoms. The structure of all synthesized compounds was fully characterized by physicochemical, spectroscopic and single crystal X-ray diffraction analysis techniques. The physical, spectral and analytical data of the newly synthesized metal complexes have shown the formation of 1:2 (metal:ligand) ratio. The benzoylthiourea ligands coordinate with metal atoms through oxygen and sulphur atoms. The metal atoms are in slightly distorted square-planar coordination geometry in Ni(II) or Cu(II) complex. Two oxygen and two sulphur atoms are mutually cis to each other in Ni(II) or Cu(II) complex. The intermolecular contacts in the compounds, which are HL1 and HL3, were examined by Hirshfeld surfaces and fingerprint plots using the data obtained from X-ray single crystal diffraction measurement. Besides these, their antimicrobial activities against Gram-positive bacteria (Bacillus subtilis, Staphylococcus aureus, Streptococcus pyogenes and Enterococcus faecalis) and Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) and anti-yeast activity (Candida glabrata, Candida parapsilosis and Candida albicans) were investigated. This exhibited some promising results towards testing organism. Among all the compounds, Ni(L1)2 complex showed high activity against Bacillus subtilis with MIC values at 7.81 μg/mL.

  1. Crystal structures of two erbium(III complexes with 4-aminobenzoic acid and 4-chloro-3-nitrobenzoic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2015-12-01

    Full Text Available The crystal structures of two erbium(III complexes with 4-aminobenzoic acid (4-ABAH, namely bis(μ2-4-aminobenzoato-κ2O:O′bis[bis(4-aminobenzoato-κ2O,O′diaquaerbium(III] dihydrate, [Er2(C7H6NO26(H2O4]·2H2O, (I, and 4-chloro-3-nitrobenzoic acid (CLNBAH, namely poly[hexakis(μ2-4-chloro-3-nitrobenzoato-κ2O:O′bis(dimethyl sulfoxide-κOdierbium(III], [Er2(C7H3ClNO46(C2H6OS2]n, (II, have been determined. In the structure of solvatomorphic compound (I, the symmetry-related irregular ErO8 coordination polyhedra in the discrete centrosymmetric dinuclear complex comprise two monodentate water molecules and six carboxylate O-atom donors, four from two bidentate carboxylate O,O′-chelate groups and two from the bis-monodentate O:O′-bridging group of the third 4-ABA anion. The Er—O bond-length range is 2.232 (3–2.478 (3 Å and the Er...Er separation in the dinuclear complex unit is 4.7527 (4 Å. One of the coordinating water molecules is involved in an intra-unit O—H...O hydrogen-bonding association with an inversion-related carboxylate O-atom acceptor. In contrast, the anhydrous compound (II is polymeric, based on centrosymmetric dinuclear repeat units comprising ErO7 coordination polyhedra which involve four O-atom donors from two bidentate O:O′-bridging carboxylate groups, one O-atom donor from the monodentate dimethyl sulfoxide ligand and two O-atom donors from the third bridging CLNBA anion. The latter provides the inter-unit link in the one-dimensional coordination polymer extending along [100]. The Er—O bond-length range in (II is 2.239 (6–2.348 (6 Å and the Er...Er separation within the dinuclear unit is 4.4620 (6 Å. In the crystal of (I, extensive inter-dimer O—H...O and N—H...O hydrogen-bonding interactions involving both the coordinating water molecules and the solvent water molecules, as well as the amine groups of the 4-ABA anions, give an overall three-dimensional network structure. Within

  2. Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model

    Directory of Open Access Journals (Sweden)

    Alexander Gabriëlse

    2017-11-01

    Full Text Available In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO lattices not previously considered for the square shoulder model.

  3. Synthesis and X-ray structure of the dysprosium(III) complex derived ...

    African Journals Online (AJOL)

    Synthesis and X-ray structure of the dysprosium(III) complex derived from the ligand 5-chloro-1 ... Bulletin of the Chemical Society of Ethiopia ... synthesized and its crystal structure determined by single X-ray diffraction at room temperature.

  4. Three-dimensional imaging of a complex concaved cuboctahedron copper sulfide crystal by x-ray nanotomography

    International Nuclear Information System (INIS)

    Chen Jie; Tian Jinping; Li Wenjie; Tian Yangchao; Wu Chunyan; Yu Shuhong

    2008-01-01

    By combining Fresnel zone-plate based transmission x-ray microscopy with computed tomography, the nanoscale features in materials with complex shapes can be imaged using synchrotron radiation. The tomographic data sets of a complex copper sulfide crystal were acquired in the angle range ±70 deg. at photon energy of 8.0 keV and then were reconstructed by a standard filtered-back-projection algorithm. This experiment shows the quantifiable three-dimensional information of the copper sulfide crystal, which offers a complete understanding of the concaved cuboctahedron structure with 14 faces comprising of six squares and eight triangles

  5. Crystal structure of [NEt3H]2[TaOF5

    International Nuclear Information System (INIS)

    Furmanova, N.G.; Verin, I.A.; Zanin, I.E.; Zozulin, A.N.; Il'in, E.G.

    1991-01-01

    By means of isothermal evaporation of triethylammonium oxofluorotantalate solution crystals are grown and studied by the methods of 19 F NMR spectrocopy and X-ray diffraction analysis. The crystals grown are monoclinic, a=9.926, b=7.906, c=11.657 A, β=90.83 deg, Z=2, sp. gr. P2 1 /n. The structure is composed of [TaOF 5 ] 2- anions and [NEt 3 H] + cations bound with the anions by H-bonds. Only the Van der Waals interaction is realized between the complexes

  6. Photonic Crystal Laser-Driven Accelerator Structures

    International Nuclear Information System (INIS)

    Cowan, B

    2004-01-01

    The authors discuss simulated photonic crystal structure designs for laser-driven particle acceleration. They focus on three-dimensional planar structures based on the so-called ''woodpile'' lattice, demonstrating guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice. They introduce a candidate geometry and discuss the properties of the accelerating mode. They also discuss the linear beam dynamics in the structure present a novelmethod for focusing the beam. In addition they describe ongoing investigations of photonic crystal fiber-based structures

  7. The crystal structure of tris(thenoyltrifluoroacetonato)bis(triphenylphosphine oxide)neodymium(III)

    International Nuclear Information System (INIS)

    Leipoldt, J.G.; Bok, L.D.C.; Laubscher, A.E.; Basson, S.S.

    1975-01-01

    The crystal structure of tris(thenoyltrifluoroacetonato)bis= x (triphenylphosphine oxide)neodymium(III), (Nd(TTa) 3 .2TPPO), has been determined by single crystal X-ray diffraction. A total number of 5505 independent reflections was used for the structure determination. The complex crystallized in the triclinic space group P 1 - with two molecules in the unit cell. The cell dimensions are a = 23.64 A, b Z= 12.15 A, C 11.19 A, α = 109.4 0 , β = 104.2 0 , γ = 90.8 0 . The final calculated R vale is 8.4%. The molecule is monomeric and the neodymium atom is coordinated to eight oxygen atoms (six from the three thenoyltrifluoroacetone groups and two from the two triphenylphosphine groups) which form a dodecahedron. The average neodymium-oxygen bond length is 2.44 A. (author)

  8. Crystal structure determination of Efavirenz

    International Nuclear Information System (INIS)

    Popeneciu, Horea; Dumitru, Ristoiu; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria

    2015-01-01

    Needle-shaped single crystals of the title compound, C 14 H 9 ClF 3 NO 2 , were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring

  9. Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP-N-Acetylmuramic Acid:l-Alanine Ligase (MurC) from Haemophilus influenzae

    OpenAIRE

    Mol, Clifford D.; Brooun, Alexei; Dougan, Douglas R.; Hilgers, Mark T.; Tari, Leslie W.; Wijnands, Robert A.; Knuth, Mark W.; McRee, Duncan E.; Swanson, Ronald V.

    2003-01-01

    UDP-N-acetylmuramic acid:l-alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP-N-acetylmuramic acid (UNAM) and Mg2+ and of a fully assembled MurC complex with its product UDP-N-acetylmuramoyl-l-alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn2+ have been determined to 1.85- and 1.7-Å resolution, respective...

  10. Crystal Structure of Human Factor VIII: Implications for the Formation of the Factor IXa-Factor VIIIa Complex

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, J.C.; Huang, M.; Roth, D.A.; Furie, B.C.; Furie, B. (Wyeth); (MBL)

    2008-06-03

    Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular domains and contains one Ca{sup 2+} and two Cu{sup 2+} ions. The three homologous A domains form a triangular heterotrimer where the A1 and A3 domains serve as the base and interact with the C2 and C1 domains, respectively. The structurally homologous C1 and C2 domains reveal membrane binding features. Based on biochemical studies, a model of the factor IXa-factor VIIIa complex was constructed by in silico docking. Factor IXa wraps across the side of factor VIII, and an extended interface spans the factor VIII heavy and light chains. This model provides insight into the activation of factor VIII and the interaction of factor VIIIa with factor IXa on the membrane surface.

  11. Crystal Structure of Human Factor VIII: Implications for the Formation of the Factor IXa-Factor VIIIa Complex

    Energy Technology Data Exchange (ETDEWEB)

    Chi Ki Ngo,J.; Huang, M.; Roth, D.; Furie, B.; Furie, B.

    2008-01-01

    Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular domains and contains one Ca(2+) and two Cu(2+) ions. The three homologous A domains form a triangular heterotrimer where the A1 and A3 domains serve as the base and interact with the C2 and C1 domains, respectively. The structurally homologous C1 and C2 domains reveal membrane binding features. Based on biochemical studies, a model of the factor IXa-factor VIIIa complex was constructed by in silico docking. Factor IXa wraps across the side of factor VIII, and an extended interface spans the factor VIII heavy and light chains. This model provides insight into the activation of factor VIII and the interaction of factor VIIIa with factor IXa on the membrane surface.

  12. An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Cook, William J; Senkovich, Olga; Chattopadhyay, Debasish; (UAB)

    2009-06-08

    The structure, function and reaction mechanism of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) have been extensively studied. Based on these studies, three anion binding sites have been identified, one 'Ps' site (for binding the C-3 phosphate of the substrate) and two sites, 'Pi' and 'new Pi', for inorganic phosphate. According to the original flip-flop model, the substrate phosphate group switches from the 'Pi' to the 'Ps' site during the multistep reaction. In light of the discovery of the 'new Pi' site, a modified flip-flop mechanism, in which the C-3 phosphate of the substrate binds to the 'new Pi' site and flips to the 'Ps' site before the hydride transfer, was proposed. An alternative model based on a number of structures of B. stearothermophilus GAPDH ternary complexes (non-covalent and thioacyl intermediate) proposes that in the ternary Michaelis complex the C-3 phosphate binds to the 'Ps' site and flips from the 'Ps' to the 'new Pi' site during or after the redox step. We determined the crystal structure of Cryptosporidium parvum GAPDH in the apo and holo (enzyme + NAD) state and the structure of the ternary enzyme-cofactor-substrate complex using an active site mutant enzyme. The C. parvum GAPDH complex was prepared by pre-incubating the enzyme with substrate and cofactor, thereby allowing free movement of the protein structure and substrate molecules during their initial encounter. Sulfate and phosphate ions were excluded from purification and crystallization steps. The quality of the electron density map at 2{angstrom} resolution allowed unambiguous positioning of the substrate. In three subunits of the homotetramer the C-3 phosphate group of the non-covalently bound substrate is in the 'new Pi' site. A concomitant movement of the phosphate binding loop is observed in these three subunits. In the fourth subunit the C-3 phosphate

  13. An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme

    Directory of Open Access Journals (Sweden)

    Chattopadhyay Debasish

    2009-02-01

    Full Text Available Abstract Background The structure, function and reaction mechanism of glyceraldehyde 3-phosphate dehydrogenase (GAPDH have been extensively studied. Based on these studies, three anion binding sites have been identified, one 'Ps' site (for binding the C-3 phosphate of the substrate and two sites, 'Pi' and 'new Pi', for inorganic phosphate. According to the original flip-flop model, the substrate phosphate group switches from the 'Pi' to the 'Ps' site during the multistep reaction. In light of the discovery of the 'new Pi' site, a modified flip-flop mechanism, in which the C-3 phosphate of the substrate binds to the 'new Pi' site and flips to the 'Ps' site before the hydride transfer, was proposed. An alternative model based on a number of structures of B. stearothermophilus GAPDH ternary complexes (non-covalent and thioacyl intermediate proposes that in the ternary Michaelis complex the C-3 phosphate binds to the 'Ps' site and flips from the 'Ps' to the 'new Pi' site during or after the redox step. Results We determined the crystal structure of Cryptosporidium parvum GAPDH in the apo and holo (enzyme + NAD state and the structure of the ternary enzyme-cofactor-substrate complex using an active site mutant enzyme. The C. parvum GAPDH complex was prepared by pre-incubating the enzyme with substrate and cofactor, thereby allowing free movement of the protein structure and substrate molecules during their initial encounter. Sulfate and phosphate ions were excluded from purification and crystallization steps. The quality of the electron density map at 2Å resolution allowed unambiguous positioning of the substrate. In three subunits of the homotetramer the C-3 phosphate group of the non-covalently bound substrate is in the 'new Pi' site. A concomitant movement of the phosphate binding loop is observed in these three subunits. In the fourth subunit the C-3 phosphate occupies an unexpected site not seen before and the phosphate binding loop remains in

  14. Structural basis for the inhibition of M1 family aminopeptidases by the natural product actinonin: Crystal structure in complex with E. coli aminopeptidase N.

    Science.gov (United States)

    Ganji, Roopa Jones; Reddi, Ravikumar; Gumpena, Rajesh; Marapaka, Anil Kumar; Arya, Tarun; Sankoju, Priyanka; Bhukya, Supriya; Addlagatta, Anthony

    2015-05-01

    Actinonin is a pseudotripeptide that displays a high affinity towards metalloproteases including peptide deformylases (PDFs) and M1 family aminopeptidases. PDF and M1 family aminopeptidases belong to thermolysin-metzincin superfamily. One of the major differences in terms of substrate binding pockets between these families is presence (in M1 aminopeptidases) or absence (in PDFs) of an S1 substrate pocket. The binding mode of actinonin to PDFs has been established previously; however, it is not clear how the actinonin, without a P1 residue, would bind to the M1 aminopeptidases. Here we describe the crystal structure of Escherichia coli aminopeptidase N (ePepN), a model protein of the M1 family aminopeptidases in complex with actinonin. For comparison we have also determined the structure of ePepN in complex with a well-known tetrapeptide inhibitor, amastatin. From the comparison of the actinonin and amastatin ePepN complexes, it is clear that the P1 residue is not critical as long as strong metal chelating head groups, like hydroxamic acid or α-hydroxy ketone, are present. Results from this study will be useful for the design of selective and efficient hydroxamate inhibitors against M1 family aminopeptidases. © 2015 The Protein Society.

  15. Spin state of mixed crystals of iron with zinc or cobalt for the assembled complexes bridged by 1,3-bis(4-pyridyl)propanes

    International Nuclear Information System (INIS)

    Nakashima, S; Dote, T; Atsuchi, M; Inoue, K

    2010-01-01

    Mixed crystals, [Fe 1-x M x (NCX) 2 (bpp) 2 ] (M=Zn, Co; X=S, Se; bpp1,3-bis(4-pyridyl)propane), had a similar structure with 2D interpenetrated structure of [Fe(NCX) 2 (bpp) 2 ]. The proportion of Fe II low-spin state in the mixed crystals of NCSe complex increased compared with that of the corresponding Fe complex, while such change in the Moessbauer spectra was not observed in the NCS complex.

  16. Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum.

    Science.gov (United States)

    Bhaumik, Prasenjit; Horimoto, Yasumi; Xiao, Huogen; Miura, Takuya; Hidaka, Koushi; Kiso, Yoshiaki; Wlodawer, Alexander; Yada, Rickey Y; Gustchina, Alla

    2011-07-01

    Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1Å, respectively. The apoenzyme crystallized in the orthorhombic space group P2(1)2(1)2(1) with two molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4(3) with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes. Published by Elsevier Inc.

  17. Crystal Structure of the Thermus thermophilus 16 S rRNA Methyltransferase RsmC in Complex with Cofactor and Substrate Guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Demirci, H.; Gregory, S; Dahlberg, A; Jogl, G

    2008-01-01

    Post-transcriptional modification is a ubiquitous feature of ribosomal RNA in all kingdoms of life. Modified nucleotides are generally clustered in functionally important regions of the ribosome, but the functional contribution to protein synthesis is not well understood. Here we describe high resolution crystal structures for the N{sup 2}-guanine methyltransferase RsmC that modifies residue G1207 in 16 S rRNA near the decoding site of the 30 S ribosomal subunit. RsmC is a class I S-adenosyl-l-methionine-dependent methyltransferase composed of two methyltransferase domains. However, only one S-adenosyl-l-methionine molecule and one substrate molecule, guanosine, bind in the ternary complex. The N-terminal domain does not bind any cofactor. Two structures with bound S-adenosyl-l-methionine and S-adenosyl-l-homocysteine confirm that the cofactor binding mode is highly similar to other class I methyltransferases. Secondary structure elements of the N-terminal domain contribute to cofactor-binding interactions and restrict access to the cofactor-binding site. The orientation of guanosine in the active site reveals that G1207 has to disengage from its Watson-Crick base pairing interaction with C1051 in the 16 S rRNA and flip out into the active site prior to its modification. Inspection of the 30 S crystal structure indicates that access to G1207 by RsmC is incompatible with the native subunit structure, consistent with previous suggestions that this enzyme recognizes a subunit assembly intermediate.

  18. Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

    International Nuclear Information System (INIS)

    Gai, Zuoqi; Nakamura, Akiyoshi; Tanaka, Yoshikazu; Hirano, Nagisa; Tanaka, Isao; Yao, Min

    2013-01-01

    Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution. After crystallization of a certain protein–RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly

  19. Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

    Energy Technology Data Exchange (ETDEWEB)

    Gai, Zuoqi; Nakamura, Akiyoshi [Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Yoshikazu, E-mail: tanaka@sci.hokudai.ac.jp [Hokkaido University, Sapporo 060-0810 (Japan); Hokkaido University, Sapporo 060-0810 (Japan); Hirano, Nagisa [Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Isao; Yao, Min [Hokkaido University, Sapporo 060-0810 (Japan); Hokkaido University, Sapporo 060-0810 (Japan)

    2013-11-01

    Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution. After crystallization of a certain protein–RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly.

  20. Light-induced dynamic structural color by intracellular 3D photonic crystals in brown algae.

    Science.gov (United States)

    Lopez-Garcia, Martin; Masters, Nathan; O'Brien, Heath E; Lennon, Joseph; Atkinson, George; Cryan, Martin J; Oulton, Ruth; Whitney, Heather M

    2018-04-01

    Natural photonic crystals are responsible for strong reflectance at selective wavelengths in different natural systems. We demonstrate that intracellular opal-like photonic crystals formed from lipids within photosynthetic cells produce vivid structural color in the alga Cystoseira tamariscifolia . The reflectance of the opaline vesicles is dynamically responsive to environmental illumination. The structural color is present in low light-adapted samples, whereas higher light levels produce a slow disappearance of the structural color such that it eventually vanishes completely. Once returned to low-light conditions, the color re-emerges. Our results suggest that these complex intracellular natural photonic crystals are responsive to environmental conditions, changing their packing structure reversibly, and have the potential to manipulate light for roles beyond visual signaling.

  1. PAK4 crystal structures suggest unusual kinase conformational movements.

    Science.gov (United States)

    Zhang, Eric Y; Ha, Byung Hak; Boggon, Titus J

    2018-02-01

    In order for protein kinases to exchange nucleotide they must open and close their catalytic cleft. These motions are associated with rotations of the N-lobe, predominantly around the 'hinge region'. We conducted an analysis of 28 crystal structures of the serine-threonine kinase, p21-activated kinase 4 (PAK4), including three newly determined structures in complex with staurosporine, FRAX486, and fasudil (HA-1077). We find an unusual motion between the N-lobe and C-lobe of PAK4 that manifests as a partial unwinding of helix αC. Principal component analysis of the crystal structures rationalizes these movements into three major states, and analysis of the kinase hydrophobic spines indicates concerted movements that create an accessible back pocket cavity. The conformational changes that we observe for PAK4 differ from previous descriptions of kinase motions, and although we observe these differences in crystal structures there is the possibility that the movements observed may suggest a diversity of kinase conformational changes associated with regulation. Protein kinases are key signaling proteins, and are important drug targets, therefore understanding their regulation is important for both basic research and clinical points of view. In this study, we observe unusual conformational 'hinging' for protein kinases. Hinging, the opening and closing of the kinase sub-domains to allow nucleotide binding and release, is critical for proper kinase regulation and for targeted drug discovery. We determine new crystal structures of PAK4, an important Rho-effector kinase, and conduct analyses of these and previously determined structures. We find that PAK4 crystal structures can be classified into specific conformational groups, and that these groups are associated with previously unobserved hinging motions and an unusual conformation for the kinase hydrophobic core. Our findings therefore indicate that there may be a diversity of kinase hinging motions, and that these may

  2. Crystal structure of inactive form of Rab3B

    International Nuclear Information System (INIS)

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    2012-01-01

    Highlights: ► This is the first structural information of human Rab3B. ► To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. ► The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 Å resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  3. Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Hai, Yang; Christianson, David W.

    2016-03-16

    Leishmaniaarginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiatesde novopolyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures ofL. mexicanaarginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents,i.e.the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

  4. Crystal structures of three classes of non-steroidal anti-inflammatory drugs in complex with aldo-keto reductase 1C3.

    Directory of Open Access Journals (Sweden)

    Jack U Flanagan

    Full Text Available Aldo-keto reductase 1C3 (AKR1C3 catalyses the NADPH dependent reduction of carbonyl groups in a number of important steroid and prostanoid molecules. The enzyme is also over-expressed in prostate and breast cancer and its expression is correlated with the aggressiveness of the disease. The steroid products of AKR1C3 catalysis are important in proliferative signalling of hormone-responsive cells, while the prostanoid products promote prostaglandin-dependent proliferative pathways. In these ways, AKR1C3 contributes to tumour development and maintenance, and suggest that inhibition of AKR1C3 activity is an attractive target for the development of new anti-cancer therapies. Non-steroidal anti-inflammatory drugs (NSAIDs are one well-known class of compounds that inhibits AKR1C3, yet crystal structures have only been determined for this enzyme with flufenamic acid, indomethacin, and closely related analogues bound. While the flufenamic acid and indomethacin structures have been used to design novel inhibitors, they provide only limited coverage of the NSAIDs that inhibit AKR1C3 and that may be used for the development of new AKR1C3 targeted drugs. To understand how other NSAIDs bind to AKR1C3, we have determined ten crystal structures of AKR1C3 complexes that cover three different classes of NSAID, N-phenylanthranilic acids (meclofenamic acid, mefenamic acid, arylpropionic acids (flurbiprofen, ibuprofen, naproxen, and indomethacin analogues (indomethacin, sulindac, zomepirac. The N-phenylanthranilic and arylpropionic acids bind to common sites including the enzyme catalytic centre and a constitutive active site pocket, with the arylpropionic acids probing the constitutive pocket more effectively. By contrast, indomethacin and the indomethacin analogues sulindac and zomepirac, display three distinctly different binding modes that explain their relative inhibition of the AKR1C family members. This new data from ten crystal structures greatly broadens

  5. Crystal structures of two eukaryotic nucleases involved in RNA metabolism

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich

    RNA serves a number of functions in the cell: mRNAs are the carriers of information between gene and protein, tRNAs and rRNAs are involved in the synthesis of proteins, whereas a number of additional RNA species are responsible for other functions in the cell. The quality of the different RNAs...... RNAs. We have solved the structures of two nucleases involved in 3'-5' degradation of RNA; the S. pombe Pop2p and the S. cerevisiae Rrp6p. Pop2p is part of the main cytoplasmatic deadenylation complex in yeast, which also contains the nuclease Ccr4p. Deadenylation, where the poly(A)-tail is removed...... specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures...

  6. Expression, purification and crystallization of the ancestral androgen receptor-DHT complex.

    Science.gov (United States)

    Colucci, Jennifer K; Ortlund, Eric A

    2013-09-01

    Steroid receptors (SRs) are a closely related family of ligand-dependent nuclear receptors that mediate the transcription of genes critical for development, reproduction and immunity. SR dysregulation has been implicated in cancer, inflammatory diseases and metabolic disorders. SRs bind their cognate hormone ligand with exquisite specificity, offering a unique system to study the evolution of molecular recognition. The SR family evolved from an estrogen-sensitive ancestor and diverged to become sensitive to progestagens, corticoids and, most recently, androgens. To understand the structural mechanisms driving the evolution of androgen responsiveness, the ancestral androgen receptor (ancAR1) was crystallized in complex with 5α-dihydrotestosterone (DHT) and a fragment of the transcriptional mediator/intermediary factor 2 (Tif2). Crystals diffracted to 2.1 Å resolution and the resulting structure will permit a direct comparison with its progestagen-sensitive ancestor, ancestral steroid receptor 2 (AncSR2).

  7. Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM.

    Directory of Open Access Journals (Sweden)

    Ravi Raghav Sonani

    Full Text Available Isolated phycobilisome (PBS sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM. The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree of 0.158 (0.229 with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.

  8. Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

    Science.gov (United States)

    Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

    2018-03-01

    The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

  9. The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis.

    Science.gov (United States)

    Sasaki, Hiroshi; Kubota, Keiko; Lee, Woo C; Ohtsuka, Jun; Kojima, Masaki; Iwata, So; Nakagawa, Atsushi; Takahashi, Kenji; Tanokura, Masaru

    2012-07-01

    Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic peptidases, AGP is a unique two-chain enzyme with a light chain and a heavy chain bound non-covalently with each other, and thus is an interesting target for protein structure-function relationship studies. In this article, we report the crystal structure of a dimeric form of the enzyme at a resolution of 1.6 Å. This form has a unique structure in which the C-terminal region of the light chain of one of the molecules binds to the active site cleft of the other molecule like a part of a substrate. This form mimics the enzyme-activation product complex produced upon autoproteolysis, and provides a structural clue that could help to clarify the activation mechanism. This type of dimeric structure of a peptidase is here reported for the first time.

  10. The Gd{sub 14}Ag{sub 51} structure type and its relation to some complex amalgam structures

    Energy Technology Data Exchange (ETDEWEB)

    Tambornino, Frank; Sappl, Jonathan; Hoch, Constantin, E-mail: constantin.hoch@cup.uni-muenchen.de

    2015-01-05

    Highlights: • The Gd{sub 14}Ag{sub 51} structure type has been revisited on the basis of single crystal diffraction data. • Symmetry analysis from electron density and TEM shows the space group P6/m to be true. • Gd{sub 14}Ag{sub 51} shows good metallic behaviour. • Structure relations to alkali, alkaline-earth and rare-earth metal amalgams can be established. • Complexity values for the RE{sub 14}Ag{sub 51} structure family were calculated. - Abstract: A plethora of binary and ternary intermetallic compounds has been assigned to the Gd{sub 14}Ag{sub 51} structure type, crystallising in the hexagonal system (space group P6/m, a = 1264.30(18) pm, c = 933.58(11) pm for Gd{sub 14}Ag{sub 51}). Starting in the late 1960s, much work has been invested in the structural elucidation of these crystal structures. However, reliable single crystal data are scarce, and most structure type assignments have been performed merely on the basis of powder data. We have redetermined four representatives of the binary RE{sub 14}Ag{sub 51} structure type (RE = Y, Ce, Gd, Tb) with modern high-precision single crystal X-ray methods. The assignment of the Gd{sub 14}Ag{sub 51} structure type to space group P6/m was additionally verified by careful analysis of high resolution transmission electron micrographs. We emphasise the close relation of the Gd{sub 14}Ag{sub 51} structure type to the structures of some recently described amalgams of similar composition focussing on disorder phenomena and structural complexity. Furthermore, we provide detailed information on synthesis as well as electrical and magnetic properties for Gd{sub 14}Ag{sub 51}, the parent compound of this structure family.

  11. Synthesis and Crystal Structures of Luminescent Mononuclear Ni(ii and Cd(ii Complexes with 1,10-phenanthroline

    Directory of Open Access Journals (Sweden)

    Ecaterina Tocana

    2017-12-01

    Full Text Available New supramolecular systems of Ni(II and Cd(II with 1,10-phenanthroline constructed by non-covalent interactions have been synthesized and characterized by single-crystal X-ray diffractometry. The smaller nickel(II ion forms a cis complex with outer-sphere perchlorates, while the cadmium(II ion forms a trans complex involving inner-sphere perchlorates. Both compoundsrevealintraligand-basedluminescentproperties.

  12. Method of fabricating patterned crystal structures

    KAUST Repository

    Yu, Liyang

    2016-12-15

    A method of manufacturing a patterned crystal structure for includes depositing an amorphous material. The amorphous material is modified such that a first portion of the amorphous thin-film layer has a first height/volume and a second portion of the amorphous thin-film layer has a second height/volume greater than the first portion. The amorphous material is annealed to induce crystallization, wherein crystallization is induced in the second portion first due to the greater height/volume of the second portion relative to the first portion to form patterned crystal structures.

  13. Purification and crystallization of dengue and West Nile virus NS2B–NS3 complexes

    Energy Technology Data Exchange (ETDEWEB)

    D’Arcy, Allan, E-mail: allan.darcy@novartis.com; Chaillet, Maxime; Schiering, Nikolaus; Villard, Frederic [Novartis Institutes of Biomedical Research, Protease Platform, Klybeckstrasse 144, CH 4002 Basel (Switzerland); Lim, Siew Pheng [Novartis Institutes of Tropical Diseases (Singapore); Lefeuvre, Peggy [Novartis Institutes of Biomedical Research, Protease Platform, Klybeckstrasse 144, CH 4002 Basel (Switzerland); Erbel, Paul [Novartis Institutes of Biomedical Research, Protease Platform, Klybeckstrasse 144, CH 4002 Basel (Switzerland); Novartis Institutes of Tropical Diseases (Singapore)

    2006-02-01

    Crystals of dengue serotype 2 and West Nile virus NS2B–NS3 protease complexes have been obtained and the crystals of both diffract to useful resolution. Sample homogeneity was essential for obtaining X-ray-quality crystals of the dengue protease. Controlled proteolysis produced a crystallizable fragment of the apo West Nile virus NS2B–NS3 and crystals were also obtained in the presence of a peptidic inhibitor. Both dengue and West Nile virus infections are an increasing risk to humans, not only in tropical and subtropical areas, but also in North America and parts of Europe. These viral infections are generally transmitted by mosquitoes, but may also be tick-borne. Infection usually results in mild flu-like symptoms, but can also cause encephalitis and fatalities. Approximately 2799 severe West Nile virus cases were reported this year in the United States, resulting in 102 fatalities. With this alarming increase in the number of West Nile virus infections in western countries and the fact that dengue virus already affects millions of people per year in tropical and subtropical climates, there is a real need for effective medicines. A possible therapeutic target to combat these viruses is the protease, which is essential for virus replication. In order to provide structural information to help to guide a lead identification and optimization program, crystallizations of the NS2B–NS3 protease complexes from both dengue and West Nile viruses have been initiated. Crystals that diffract to high resolution, suitable for three-dimensional structure determinations, have been obtained.

  14. Purification and crystallization of dengue and West Nile virus NS2B–NS3 complexes

    International Nuclear Information System (INIS)

    D’Arcy, Allan; Chaillet, Maxime; Schiering, Nikolaus; Villard, Frederic; Lim, Siew Pheng; Lefeuvre, Peggy; Erbel, Paul

    2006-01-01

    Crystals of dengue serotype 2 and West Nile virus NS2B–NS3 protease complexes have been obtained and the crystals of both diffract to useful resolution. Sample homogeneity was essential for obtaining X-ray-quality crystals of the dengue protease. Controlled proteolysis produced a crystallizable fragment of the apo West Nile virus NS2B–NS3 and crystals were also obtained in the presence of a peptidic inhibitor. Both dengue and West Nile virus infections are an increasing risk to humans, not only in tropical and subtropical areas, but also in North America and parts of Europe. These viral infections are generally transmitted by mosquitoes, but may also be tick-borne. Infection usually results in mild flu-like symptoms, but can also cause encephalitis and fatalities. Approximately 2799 severe West Nile virus cases were reported this year in the United States, resulting in 102 fatalities. With this alarming increase in the number of West Nile virus infections in western countries and the fact that dengue virus already affects millions of people per year in tropical and subtropical climates, there is a real need for effective medicines. A possible therapeutic target to combat these viruses is the protease, which is essential for virus replication. In order to provide structural information to help to guide a lead identification and optimization program, crystallizations of the NS2B–NS3 protease complexes from both dengue and West Nile viruses have been initiated. Crystals that diffract to high resolution, suitable for three-dimensional structure determinations, have been obtained

  15. Synthesis, crystal structure and thermal decomposition mechanism of the complex [Sm(p-BrBA)3bipy.H2O]2.H2O

    International Nuclear Information System (INIS)

    Zhang Haiyan; Zhang Jianjun; Ren Ning; Xu Suling; Tian Liang; Bai Jihai

    2008-01-01

    A new binuclear samarium (III) complex [Sm(p-BrBA) 3 bipy.H 2 O] 2 .H 2 O (p-BrBA = p-bromobenzoic acid; bipy = 2,2'-bipyridine) has been synthesized and characterized by elemental analysis, UV, IR, molar conductance and TG-DTG techniques. The structure of the complex was established by single crystal X-ray diffraction. It crystallizes in triclinic, space group P1-bar with a = 8.2476(7) A, b = 13.3483(10) A, c = 15.9035(13) A, α 73.9160(10) o , β = 78.9630(10) o , γ = 74.4770(10) o , Z = 1, D c 1.947 g cm -3 , F(000) = 910. The carboxylic groups are bonded to the samarium ion in two modes: bidentate bridging, monodentate. Each center Sm 3+ ion is eight-coordinated by one 2,2'-bipyridine molecular, four bidentate bridging and a monodentate carboxylic group, as well as one water molecular. The coordination polyhedron around each Sm 3+ ion can be described as bi-capped triangular prism geometry. The thermal decomposition behavior of the title complex in a static air atmosphere was investigated by TG-DTG and IR techniques

  16. Purification, crystallization and preliminary X-ray analysis of a Nup107–Nup133 heterodimeric nucleoporin complex

    International Nuclear Information System (INIS)

    Boehmer, Thomas; Schwartz, Thomas U.

    2007-01-01

    A heterodimeric complex consisting of the C-terminal domains of human nucleoporins Nup107 and Nup133 was purified and crystallized and complete diffraction data sets were collected. The nuclear pore complex (NPC), the sole gateway of traffic between the nucleus and the cytoplasm, is built up from multiple copies of about 30 proteins collectively termed nucleoporins (nups). Nups are organized into distinct subcomplexes. Nup107 and Nup133 are members of the essential Nup107–160 subcomplex, a component of the central NPC architecture. A dimeric complex of the C-terminal domains of human Nup107 and Nup133 was expressed from a bicistronic vector in Escherichia coli, purified and crystallized in two different crystal forms. Crystals grown in the presence of 18–22% PEG 3350 belong to space group P2 1 2 1 2 1 and diffracted to 2.9 Å. Native and seleno-l-methionine-derivative crystals grown in the presence of 1.1 M sodium malonate belong to space group C2 and diffracted to 2.55 and 2.9 Å, respectively. Structure determination of this complex will give the first insights into the protein–protein interactions within a core module of the NPC

  17. Purification, crystallization and preliminary X-ray analysis of a Nup107–Nup133 heterodimeric nucleoporin complex

    Energy Technology Data Exchange (ETDEWEB)

    Boehmer, Thomas; Schwartz, Thomas U., E-mail: tus@mit.edu [Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States)

    2007-09-01

    A heterodimeric complex consisting of the C-terminal domains of human nucleoporins Nup107 and Nup133 was purified and crystallized and complete diffraction data sets were collected. The nuclear pore complex (NPC), the sole gateway of traffic between the nucleus and the cytoplasm, is built up from multiple copies of about 30 proteins collectively termed nucleoporins (nups). Nups are organized into distinct subcomplexes. Nup107 and Nup133 are members of the essential Nup107–160 subcomplex, a component of the central NPC architecture. A dimeric complex of the C-terminal domains of human Nup107 and Nup133 was expressed from a bicistronic vector in Escherichia coli, purified and crystallized in two different crystal forms. Crystals grown in the presence of 18–22% PEG 3350 belong to space group P2{sub 1}2{sub 1}2{sub 1} and diffracted to 2.9 Å. Native and seleno-l-methionine-derivative crystals grown in the presence of 1.1 M sodium malonate belong to space group C2 and diffracted to 2.55 and 2.9 Å, respectively. Structure determination of this complex will give the first insights into the protein–protein interactions within a core module of the NPC.

  18. Synthesis, Crystal Structure, and Luminescence Properties of a New Calcium(II Coordination Polymer Based on L-Malic Acid

    Directory of Open Access Journals (Sweden)

    Duraisamy Senthil Raja

    2013-01-01

    Full Text Available A new calcium coordination polymer [Ca(HL-MA]n (H3L-MA = L-malic acid has been solvothermally synthesized. The structure of the newly synthesized complex has been determined by single-crystal X-ray diffraction analysis and further characterized by elemental analysis, reflectance UV-Vis & IR spectra, powder X-ray diffraction (PXRD, and thermogravimetric analysis (TGA. The single crystal structure analysis showed that the complex forms three-dimensional framework. The new Ca(II complex has displayed very high thermal stability which was inferred from TGA and PXRD results. As far as the optical property of the new complex is concerned, the complex emitted its own characteristic sensitized luminescence.

  19. Coefficient of crystal lattice matching as a parameter of substrate - crystal structure compatibility in silumins

    Directory of Open Access Journals (Sweden)

    J. Piątkowski

    2009-07-01

    Full Text Available Adding high-melting point elements (Mo, Nb, Ni, Ti, W to complex silumins results in hardening of the latter ones, owing to the formation of new intermetallic phases of the AlxMey type, with refinement of dendrites in α solution and crystals in β phase. The hardening is also due to the effect of various inoculants. An addition of the inoculant is expected to form substrates, the crystal lattice of which, or some (privileged lattice planes and interatomic spaces should bear a strong resemblance to the crystal nucleus. To verify this statement, using binary phase equilibria systems, the coefficient of crystal lattice matching, being one of the measures of the crystallographic similarity, was calculated. A compatibility of this parameter (up to 20% may decide about the structure compatibility between the substrate and crystal which, in turn, is responsible for the effectiveness of alloy modification. Investigations have proved that, given the temperature range of their formation, the density, the lattice type, and the lattice parameter, some intermetallic phases of the AlxMey type can act as substrates for the crystallisation of aluminium and silicon, and some of the silumin hardening phases.

  20. Crystal structure of inactive form of Rab3B

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Shen, Yang [Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7 (Canada); Jiao, Ronghong [Department of Function Inspection, Hebei Provincial People' s Hospital, Shijiazhuang 050051 (China); Liu, Yanli; Deng, Lingfu [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Qi, Chao, E-mail: qichao@mail.ccnu.edu.cn [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer This is the first structural information of human Rab3B. Black-Right-Pointing-Pointer To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. Black-Right-Pointing-Pointer The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 A resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  1. Spin state of mixed crystals of iron with zinc or cobalt for the assembled complexes bridged by 1,3-bis(4-pyridyl)propanes

    Energy Technology Data Exchange (ETDEWEB)

    Nakashima, S [Natural Science Center for Basic Research and Development, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526 (Japan); Dote, T; Atsuchi, M; Inoue, K, E-mail: snaka@hiroshima-u.ac.j [Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526 (Japan)

    2010-03-01

    Mixed crystals, [Fe{sub 1-x}M{sub x}(NCX){sub 2}(bpp){sub 2}] (M=Zn, Co; X=S, Se; bpp1,3-bis(4-pyridyl)propane), had a similar structure with 2D interpenetrated structure of [Fe(NCX){sub 2}(bpp){sub 2}]. The proportion of Fe{sup II} low-spin state in the mixed crystals of NCSe complex increased compared with that of the corresponding Fe complex, while such change in the Moessbauer spectra was not observed in the NCS complex.

  2. Eu(III) and Tb(III) complexes with the nonsteroidal anti-inflammatory drug carprofen: synthesis, crystal structure, and photophysical properties.

    Science.gov (United States)

    Zhou, Xianju; Zhao, Xiaoqi; Wang, Yongjie; Wu, Bing; Shen, Jun; Li, Li; Li, Qingxu

    2014-12-01

    Two new lanthanide complexes with general formula [Ln2(carprofen)6(DMF)2] (Ln = Eu (1), Tb (2), DMF = N,N-dimethylformamide, carprofen = 6-chloro-α-methylcarbazole-2-acetic acid) have been synthesized by a hydrothermal method. Complex 1 was characterized by single-crystal X-ray diffraction (XRD), and it was found to crystallize in the monoclinic space group C2/c. The coordination of the ligand to the lanthanide ion has been investigated by Fourier-transform infrared (FTIR) spectra and ultraviolet-visible (UV-vis) absorption spectra. Complex 1 emits red light, but the antenna effect of the ligand is not effective, whereas complex 2 presents intense green emission with effective energy transfer from the ligand. The different performance of the two complexes is related to the energy matching between the excited states of the lanthanide ion and the triplet state of the ligand. The intramolecular energy transfer mechanisms are also discussed.

  3. The crystal structure of the complex of Zea mays alpha subunit with a fragment of human beta subunit provides the clue to the architecture of protein kinase CK2 holoenzyme

    DEFF Research Database (Denmark)

    Battistutta, R; Sarno, S; De Moliner, E

    2000-01-01

    The crystal structure of a complex between the catalytic alpha subunit of Zea mays CK2 and a 23-mer peptide corresponding the C-terminal sequence 181-203 of the human CK2 regulatory beta subunit has been determined at 3.16-A resolution. The complex, composed of two alpha chains and two peptides, ...

  4. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus: Purification, Crystallization and Structure Determination

    International Nuclear Information System (INIS)

    Clemons, William M. Jr.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2001-01-01

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 (angstrom) resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 (angstrom) resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  5. Crystal Structure, Fluorescence Property and Theoretical Calculation of the Zn(II) Complex with o-Aminobenzoic Acid and 1,10-Phenanthroline

    International Nuclear Information System (INIS)

    Zhang, Zhongyu; Bi, Caifeng; Fan, Yuhua; Zhang, Xia; Zhang, Nan; Yan, Xingchen; Zuo, Jian

    2014-01-01

    A novel complex [Zn(phen)(o-AB) 2 ] [phen: 1,10-phenanthroline o-AB: o-aminobenzoic acid] was synthesized and characterized by elemental analysis and X-ray diffraction single-crystal analysis. The crystal crystallizes in monoclinic, space group P2(1)/c with a = 7.6397(6) A, b = 16.8761(18) A, c = 17.7713(19) A, α = 90 .deg., β = 98.9570(10) .deg., γ = 90 .deg., V = 2.2633(4) nm 3 , Z = 4, F(000) = 1064, S = 1.058, Dc = 1.520 g·cm -3 , R 1 = 0.0412, wR 2 = 0.0948, μ = 1.128 mm -1 . The Zn(II) is six coordinated by two nitrogen and four oxygen atoms from the 1,10-phenanthroline and o-aminobenzoic acid to furnish a distorted octahedron geometry. The complex exhibits intense fluorescence at room temperature. Theoretical studies of the title complex were carried out by density functional theory (DFT) B3LYP method. CCDC: 898291

  6. The crystal structure and twinning of neodymium gallium perovskite single crystals

    International Nuclear Information System (INIS)

    Ubizskii, S.B.; Vasylechko, L.O.; Savytskii, D.I.; Matkovskii, A.O.; Syvorotka, I.M.

    1994-01-01

    By means of X-ray structure analysis, the crystal structure of neodymium gallium perovskite (NGP) single crystals (NdGaO 3 ) being used as a substrate for HTSC film epitaxy has been refined and the position of atoms has been determined. The possibility of YBa 2 Cu 3 O 7-x film epitaxy on the plane (110) of NGP crystal as well as its advantages and pitfalls are analysed from structural data. The twinning types in the NGP crystal were established. The twinning structure of NGP substrates is found to be stable up to a temperature of 1173 K, as differentiated from the LaGaO 3 and LaAlO 3 substrates. It is intimated that the twinning in the NGP substrates oriented as (001) can result in creation of 90 degrees twin bonds in a film, and in the case of (110)-oriented plates it is possible to ignore the twinning presence in substrate completely. (author)

  7. Crystallization of Doc and the Phd–Doc toxin–antitoxin complex

    International Nuclear Information System (INIS)

    Garcia-Pino, Abel; Dao-Thi, Minh-Hoa; Gazit, Ehud; Magnuson, Roy David; Wyns, Lode; Loris, Remy

    2008-01-01

    Crystals of bacteriophage P1 Doc were grown in the free state, in complex with a 22-amino-acid C-terminal peptide of Phd and in complex with full-length Phd. The phd/doc addiction system is responsible for the stable inheritance of lysogenic bacteriophage P1 in its plasmidic form in Escherichia coli and is the archetype of a family of bacterial toxin–antitoxin modules. The His66Tyr mutant of Doc (Doc H66Y ) was crystallized in space group P2 1 , with unit-cell parameters a = 53.1, b = 198.0, c = 54.1 Å, β = 93.0°. These crystals diffracted to 2.5 Å resolution and probably contained four dimers of Doc in the asymmetric unit. Doc H66Y in complex with a 22-amino-acid C-terminal peptide of Phd (Phd 52-73Se ) was crystallized in space group C2, with unit-cell parameters a = 111.1, b = 38.6, c = 63.3 Å, β = 99.3°, and diffracted to 1.9 Å resolution. Crystals of the complete wild-type Phd–Doc complex belonged to space group P3 1 21 or P3 2 21, had an elongated unit cell with dimensions a = b = 48.9, c = 354.9 Å and diffracted to 2.4 Å resolution using synchrotron radiation

  8. Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua; Jiang, Jiansheng; Salon, Jozef; Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Weber, Irene T.; Huang, Zhen, E-mail: huang@gsu.edu [Georgia State University, Atlanta, GA 30303 (United States)

    2014-02-01

    Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

  9. Local structural ordering in surface-confined liquid crystals

    Science.gov (United States)

    Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

    2017-06-01

    The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

  10. First principles investigation of the structure of a bacteriochlorophyll crystal

    Energy Technology Data Exchange (ETDEWEB)

    Marchi, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)]|[Centre d`Etudes Saclay, Gif-sur-Yvette (France); Hutter, J.; Parrinello, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  11. Crystal Structure of the Pseudomonas aeruginosa BEL-1 Extended-Spectrum β-Lactamase and Its Complexes with Moxalactam and Imipenem.

    Science.gov (United States)

    Pozzi, Cecilia; De Luca, Filomena; Benvenuti, Manuela; Poirel, Laurent; Nordmann, Patrice; Rossolini, Gian Maria; Mangani, Stefano; Docquier, Jean-Denis

    2016-12-01

    BEL-1 is an acquired class A extended-spectrum β-lactamase (ESBL) found in Pseudomonas aeruginosa clinical isolates from Belgium which is divergent from other ESBLs (maximum identity of 54% with GES-type enzymes). This enzyme is efficiently inhibited by clavulanate, imipenem, and moxalactam. Crystals of BEL-1 were obtained at pH 5.6, and the structure of native BEL-1 was determined from orthorhombic and monoclinic crystal forms at 1.60-Å and 1.48-Å resolution, respectively. By soaking native BEL-1 crystals, complexes with imipenem (monoclinic form, 1.79-Å resolution) and moxalactam (orthorhombic form, 1.85-Å resolution) were also obtained. In the acyl-enzyme complexes, imipenem and moxalactam differ by the position of the α-substituent and of the carbonyl oxygen (in or out of the oxyanion hole). More surprisingly, the Ω-loop, which includes the catalytically relevant residue Glu166, was found in different conformations in the various subunits, resulting in the Glu166 side chain being rotated out of the active site or even in displacement of its Cα atom up to approximately 10 Å. A BEL-1 variant showing the single Leu162Phe substitution (BEL-2) confers a higher level of resistance to CAZ, CTX, and FEP and shows significantly lower K m values than BEL-1, especially with oxyiminocephalosporins. BEL-1 Leu162 is located at the beginning of the Ω-loop and is surrounded by Phe72, Leu139, and Leu148 (contact distances, 3.5 to 3.9 Å). This small hydrophobic cavity could not reasonably accommodate the bulkier Phe162 found in BEL-2 without altering neighboring residues or the Ω-loop itself, thus likely causing an important alteration of the enzyme kinetic properties. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. Crystal structure of the potassium-importing KdpFABC membrane complex

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Ching-Shin; Pedersen, Bjørn Panyella; Stokes, David L.

    2017-06-21

    Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four-subunit potassium pump that maintains intracellular homeostasis, cell shape and turgor under conditions in which potassium is limiting1. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the superfamily of potassium transporters and another pump-like subunit (KdpB) belonging to the superfamily of P-type ATPases. Although there is considerable structural and functional information about members of both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA and a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. On the basis of these observations, we propose a mechanism that repurposes protein channel architecture for active transport across biomembranes.

  13. Crystal structures of monoamine oxidase B in complex with four inhibitors of the N-propargylaminoindan class.

    Science.gov (United States)

    Binda, Claudia; Hubálek, Frantisek; Li, Min; Herzig, Yaacov; Sterling, Jeffrey; Edmondson, Dale E; Mattevi, Andrea

    2004-03-25

    Monoamine oxidase B (MAO B) is an outer mitochondrial membrane enzyme that catalyzes the oxidation of arylalkylamine neurotransmitters. The crystal structures of MAO B in complex with four of the N-propargylaminoindan class of MAO covalent inhibitors (rasagiline, N-propargyl-1(S)-aminoindan, 6-hydroxy-N-propargyl-1(R)-aminoindan, and N-methyl-N-propargyl-1(R)-aminoindan) have been determined at a resolution of better than 2.1 A. Rasagiline, 6-hydroxy-N-propargyl-1(R)-aminoindan, and N-methyl-N-propargyl-1(R)-aminoindan adopt essentially the same conformation with the extended propargyl chain covalently bound to the flavin and the indan ring located in the rear of the substrate cavity. N-Propargyl-1(S)-aminoindan binds with the indan ring in a flipped conformation with respect to the other inhibitors, which causes a slight movement of the Tyr326 side chain. Four ordered water molecules are an integral part of the active site and establish H-bond interactions to the inhibitor atoms. These structural studies may guide future drug design to improve selectivity and efficacy by introducing appropriate substituents on the rasagiline molecular scaffold.

  14. Magnetic activity at infrared frequencies in structured metallic photonic crystals

    International Nuclear Information System (INIS)

    O'Brien, S.; Pendry, J.P.

    2002-01-01

    We derive the effective permeability and permittivity of a nanostructured metallic photonic crystal by analysing the complex reflection and transmission coefficients for slabs of various thicknesses. These quantities were calculated using the transfer matrix method. Our results indicate that these structures could be used to realize a negative effective permeability, at least up to infrared frequencies. The origin of the negative permeability is a resonance due to the internal inductance and capacitance of the structure. We also present an analytic model for the effective permeability of the crystal. The model reveals the importance of the inertial inductance due to the finite mass of the electrons in the metal. We find that this contribution to the inductance has implications for the design of metallic magnetic structures in the optical region of the spectrum. We show that the magnetic activity in the structure is accompanied by the concentration of the incident field energy into very small volumes within the structure. This property will allow us to considerably enhance non-linear effects with minute quantities of material. (author)

  15. Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose

    Energy Technology Data Exchange (ETDEWEB)

    Brzezinski, Krzysztof [Argonne National Laboratory, Argonne, IL 60439 (United States); Polish Academy of Sciences, 61-704 Poznan (Poland); Dauter, Zbigniew [Argonne National Laboratory, Argonne, IL 60439 (United States); Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl [Polish Academy of Sciences, 61-704 Poznan (Poland); A. Mickiewicz University, 60-780 Poznan (Poland); Argonne National Laboratory, Argonne, IL 60439 (United States)

    2012-02-01

    Crystal structures of the bacterial α1,6-fucosyltransferase NodZ in complex with GDP and GDP-fucose are presented. Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5′-diphosphate-β-l-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Å resolution. The fucose residue is exposed to solvent and is disordered. The enzyme–product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-l-glucosamine (penta-NAG). The structure has been determined at 1.98 Å resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop

  16. Metal complexes of salicylhydroxamic acid (H2Sha), anthranilic hydroxamic acid and benzohydroxamic acid. Crystal and molecular structure of [Cu(phen)2(Cl)]Cl x H2Sha, a model for a peroxidase-inhibitor complex.

    Science.gov (United States)

    O'Brien, E C; Farkas, E; Gil, M J; Fitzgerald, D; Castineras, A; Nolan, K B

    2000-04-01

    Stability constants of iron(III), copper(II), nickel(II) and zinc(II) complexes of salicylhydroxamic acid (H2Sha), anthranilic hydroxamic acid (HAha) and benzohydroxamic acid (HBha) have been determined at 25.0 degrees C, I=0.2 mol dm(-3) KCl in aqueous solution. The complex stability order, iron(III) > copper(II) > nickel(II) approximately = zinc(II) was observed whilst complexes of H2Sha were found to be more stable than those of the other two ligands. In the preparation of ternary metal ion complexes of these ligands and 1,10-phenanthroline (phen) the crystalline complex [Cu(phen)2(Cl)]Cl x H2Sha was obtained and its crystal structure determined. This complex is a model for hydroxamate-peroxidase inhibitor interactions.

  17. Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod–Zwilch–ZW10 (RZZ) complex

    Energy Technology Data Exchange (ETDEWEB)

    Altenfeld, Anika; Wohlgemuth, Sabine [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); Wehenkel, Annemarie [Institut Curie, CNRS UMR 3348/INSERM U1005, Bâtiment 110, Centre Universitaire, 91405 Orsay CEDEX (France); Vetter, Ingrid R. [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); Musacchio, Andrea, E-mail: andrea.musacchio@mpi-dortmund.mpg.de [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); University of Duisburg-Essen, Universitätstrasse 1, 45141 Essen (Germany)

    2015-03-20

    The 800 kDa complex of the human Rod, Zwilch and ZW10 proteins (the RZZ complex) was reconstituted in insect cells, purified, crystallized and subjected to preliminary X-ray diffraction analysis. The spindle-assembly checkpoint (SAC) monitors kinetochore–microtubule attachment during mitosis. In metazoans, the three-subunit Rod–Zwilch–ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1–Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ complex was purified to homogeneity and subjected to systematic crystallization attempts. Initial crystals containing the entire RZZ complex were obtained using the sitting-drop method and were subjected to optimization to improve the diffraction resolution limit. The crystals belonged to space group P3{sub 1} (No. 144) or P3{sub 2} (No. 145), with unit-cell parameters a = b = 215.45, c = 458.7 Å, α = β = 90.0, γ = 120.0°.

  18. Synthesis, Crystal Structure, Luminescence, Electrochemical and Antimicrobial Properties of Bis(salamo-Based Co(II Complex

    Directory of Open Access Journals (Sweden)

    Li Wang

    2017-09-01

    Full Text Available A newly designed Co(II complex, [Co3(L(OAc2(CH3OH2]·CH3OH, by the reaction of a bis(salamo-type tetraoxime ligand (H4L with Co(II acetate tetrahydrate was synthesized and characterized by elemental analyses, IR, UV-vis spectra and single-crystal X-ray crystallography. The UV-vis titration experiment manifested that a trinuclear (L:M = 1:3 complex was formed. It is worth noting that the two terminal Co(II (Co1 and Co3 atoms of the Co(II complex have different coordination modes and geometries unreported earlier. Furthermore, through intermolecular interactions (C–H···O, C–H···π and O–H···O, a 2D layer-like network is constructed. In addition, the fluorescence behaviors, antimicrobial activities and electrochemical properties of H4L and its Co(II complex were investigated.

  19. Phenoxo bridged dinuclear Zn(II) Schiff base complex as new precursor for preparation zinc oxide nanoparticles: Synthesis, characterization, crystal structures and photoluminescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Saeednia, S., E-mail: sami_saeednia@yahoo.com [Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of); Iranmanesh, P. [Department of physics, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of); Ardakani, M. Hatefi; Mohammadi, M.; Norouzi, Gh. [Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of)

    2016-06-15

    Highlights: • A novel nano-scale Zn(II) complex was synthesized by solvothermal method. • Chemical structure of the nanostructures was characterized as well as bulk complex. • The photoluminescence property of the complex was investigated at room temperature. • The thermogravimetry and differential thermal analysis were carried out. • Thermal decomposition of the nanostructures was prepared zinc oxide nanoparticles. - Abstract: Nanoparticles of a novel Zn(II) Schiff base complex, [Zn(HL)NO{sub 3}]{sub 2} (1), (H{sub 2}L = 2-[(2-hydroxy-propylimino) methyl] phenol), was synthesized by using solvothermal method. Shape, morphology and chemical structure of the synthesized nanoparticles were characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier Transform Infrared Spectoscopy (FT-IR) and UV–vis spectroscopy. Structural determination of compound 1 was determined by single-crystal X-ray diffraction. The results were revealed that the zinc complex is a centrosymmetric dimer in which deprotonated phenolates bridge the two five-coordinate metal atoms and link the two halves of the dimer. The thermal stability of compound 1 was analyzed by thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effect of the initial substrates concentration and reaction time on size and morphology of compound 1 nanostructure was investigated as well. Furthermore, the luminescent properties of the complex 1 were examined. ZnO nanoparticles with diameter between 15 and 20 nm were simply synthesized by solid-state transformation of compound 1 at 700 °C.

  20. A new tridentate Schiff base Cu(II) complex: synthesis, experimental and theoretical studies on its crystal structure, FT-IR and UV-Visible spectra.

    Science.gov (United States)

    Saheb, Vahid; Sheikhshoaie, Iran; Setoodeh, Nasim; Rudbari, Hadi Amiri; Bruno, Giuseppe

    2013-06-01

    A new Cu(II) complex [Cu(L)(NCS)] has been synthesized, using 1-(N-salicylideneimino)-2-(N,N-methyl)-aminoethane as tridentate ONN donor Schiff base ligand (HL). The dark green crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FT-IR) and UV-Visible spectra. Electronic structure calculations at the B3LYP and MP2 levels of theory are performed to optimize the molecular geometry and to calculate the UV-Visible and FT-IR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TD-DFT) method is used to calculate the electronic transitions of the complex. A scaling factor of 1.015 is obtained for vibrational frequencies computed at the B3LYP level using basis sets 6-311G(d,p). It is found that solvent has a profound effect on the electronic absorption spectrum. The UV-Visible spectrum of the complex recorded in DMSO and DMF solution can be correctly predicted by a model in which DMSO and DMF molecules are coordinated to the central Cu atom via their oxygen atoms. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Crystallization and preliminary X-ray analysis of birch-pollen allergen Bet v 1 in complex with a murine monoclonal IgG Fab' fragment

    DEFF Research Database (Denmark)

    Spangfort, M D; Mirza, Osman Asghar; Gajhede, M

    1999-01-01

    of the clinical symptoms of allergy. In order to study the structural basis of allergen-antibody interaction, a complex between the major birch-pollen allergen Bet v 1 and a Fab' fragment isolated from the murine monoclonal Bet v 1 antibody BV16 has been crystallized. Complex crystals belong to space group P1...

  2. Synthesis, crystal structures, molecular docking, and in vitro biological activities evaluation of transition metal complexes with 4-(3,4-dichlorophenyl) piperazine-1-carboxylic acid

    Science.gov (United States)

    Chen, Zhi-Jian; Chen, Ya-Na; Xu, Chun-Na; Zhao, Shan-Shan; Cao, Qi-Yue; Qian, Shao-Song; Qin, Jie; Zhu, Hai-Liang

    2016-08-01

    Three novel mononuclear complexes, [MⅡ(L)2·2H2O], (M = Cu, Ni or Cd; HL = 4-(3,4-dichlorophenyl)piperazine-1-carboxylic acid)were synthesized and structurally determined by single-crystal X-ray diffraction. Molecular docking study preliminarily revealed that complex 1 had potential urease inhibitory activity. In accordance with the result of calculation, in vitro tests of the inhibitory activities of complexes 1-3 against jack bean urease showed complex 1 (IC50 = 8.17 ± 0.91 μM) had better inhibitory activities than the positive reference acetohydroxamic acid (AHA) (IC50 = 26.99 ± 1.43 μM), while complexes 2 and 3 showed no inhibitory activities., kinetics study was carried out to explore the mechanism of the inhibiting of the enzyme, and the result indicated that complex 1 was a competitive inhibitor of urease. Albumin binding experiment and in vitro toxicity evaluation of complex 1 were implemented to explore its Pharmacological properties.

  3. Crystal structures and luminescence properties of two Cd(II) complexes based on 2-(1H-imidazol-1methyl)-6-methyl-1H-benzimidazole

    International Nuclear Information System (INIS)

    Zhang, Yuhong; Meng, Xiangru; Wen, Yu; Li, Peng; Ma, Lin; Zhang, Qiuju

    2015-01-01

    Two new complexes, {[Cd(immb)I 2 ].DMF} n (1) and {[Cd 3 (immb)(btc) 2 ]. H 2 O} n (2) (immb = 2-(1H-imidazol- 1-methyl)-6-methyl-1H-benzimidazole, btc = 1,2,3-benzenetricarboxylate, DMF = dimethyl formamide), have been synthesized and characterized. Single crystal X-ray diffraction shows that 1 exhibits a chain structure constructed by immb ligands bridging Cd(II) ions. In 2, Cd(II) ions are linked by immb ligands with bridging mode and btc3- anions with the μ 2 -η 2 :η 1 bonding pattern leading to a 2D structure. Luminescent properties have been investigated in the solid state at room temperature.

  4. Synthesis of the hexaamine ligand 1,4,7-tris(3-aminopropyl)-1,4,7-triazacyclononane: Reactivity and x-ray crystal structures of the nickel(II) and cobalt(III) complexes

    International Nuclear Information System (INIS)

    Bushnell, G.W.; Fortier, D.G.; McAuley, A.

    1988-01-01

    The synthesis of the ligand 1,4,7-tris(3-aminopropyl)-1,4,7-triazacyclononane(tapacn) can be achieved by the reaction of 1,4,7-triazacyclononane with an excess of acetonitrile, followed by reduction of the nitrile with sodium metal in toluene. Halide salts of the cobalt(III)(complex A) and nickel(II)(complex B) ions have been prepared and examined by using x-ray crystallography. The crystal structures are reported. The 13 C NMR spectrum of the dismagnetic d 6 Co(III) complex ion is reported. A discussion of the two ligand structures deals with the ligand opening and with trigonal twist angle as related to metal ion size and mechanism for redox processes of the complex. 45 refs., 6 figs., 9 tabs

  5. Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

    Energy Technology Data Exchange (ETDEWEB)

    Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke; Lam, Angela M.; Grice, Rena L.; Du, Jinfa; Sofia, Michael J.; Furman, Philip A.; Otto, Michael J. (Pharmasset); (Emerald)

    2012-08-01

    The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.

  6. Synthesis, X-ray crystal structures, and phosphate ester cleavage properties of bis(2-pyridylmethyl)amine copper(II) complexes with guanidinium pendant groups.

    Science.gov (United States)

    Belousoff, Matthew J; Tjioe, Linda; Graham, Bim; Spiccia, Leone

    2008-10-06

    Three new derivatives of bis(2-pyridylmethyl)amine (DPA) featuring ethylguanidinium (L (1)), propylguanidinium (L (2)), or butylguanidinium (L (3)) pendant groups have been prepared by the reaction of N, N- bis(2-pyridylmethyl)alkane-alpha,omega-diamines with 1 H-pyrazole-1-carboxamidine hydrochloride. The corresponding mononuclear copper(II) complexes were prepared by reacting the ligands with copper(II) nitrate and were isolated as [Cu(LH (+))(OH 2)](ClO 4) 3. xNaClO 4. yH 2O ( C1: L = L (1), x = 2, y = 3; C2: L = L (2), x = 2, y = 4; C3: L = L (3), x = 1, y = 0) following cation exchange purification. Recrystallization yielded crystals of composition [Cu(LH (+))(X)](ClO 4) 3.X ( C1': L = L (1), X = MeOH; C2': L = L (2), X = H 2O; C3': L = L (3), X = H 2O), which were suitable for X-ray crystallography. The crystal structures of C1', C2', and C3' indicate that the DPA moieties of the ligands coordinate to the copper(II) centers in a meridional fashion, with a water or methanol molecule occupying the fourth basal position. Weakly bound perchlorate anions located in the axial positions complete the distorted octahedral coordination spheres. The noncoordinating, monoprotonated guanidinium groups project away from the Cu(II)-DPA units and are involved in extensive charge-assisted hydrogen-bonding interactions with cocrystallized water/methanol molecules and perchlorate anions within the crystal lattices. The copper(II) complexes were tested for their ability to promote the cleavage of two model phosphodiesters, bis( p-nitrophenyl)phosphate (BNPP) and uridine-3'- p-nitrophenylphosphate (UpNP), as well as supercoiled plasmid DNA (pBR 322). While the presence of the guanidine pendants was found to be detrimental to BNPP cleavage efficiency, the functionalized complexes were found to cleave plasmid DNA and, in some cases, the model ribose phosphate diester, UpNP, at a faster rate than the parent copper(II) complex of DPA.

  7. Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands.

    Science.gov (United States)

    Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S; Damborsky, Jiri; Smatanova, Ivana Kuta

    2011-02-01

    Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon-halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2(1)2(1)2(1) as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively.

  8. Synthesis, crystal structure investigation and magnetism of the complex metal-rich boride series Crx(Rh1-yRuy)7-xB3 (x=0.88-1; y=0-1) with Th7Fe3-type structure

    Science.gov (United States)

    Misse, Patrick R. N.; Mbarki, Mohammed; Fokwa, Boniface P. T.

    2012-08-01

    Powder samples and single crystals of the new complex boride series Crx(Rh1-yRuy)7-xB3 (x=0.88-1; y=0-1) have been synthesized by arc-melting the elements under purified argon atmosphere on a water-cooled copper crucible. The products, which have metallic luster, were structurally characterized by single-crystal and powder X-ray diffraction as well as EDX measurements. Within the whole solid solution range the hexagonal Th7Fe3 structure type (space group P63mc, no. 186, Z=2) was identified. Single-crystal structure refinement results indicate the presence of chromium at two sites (6c and 2b) of the available three metal Wyckoff sites, with a pronounced preference for the 6c site. An unexpected Rh/Ru site preference was found in the Ru-rich region only, leading to two different magnetic behaviors in the solid solution: The Rh-rich region shows a temperature-independent (Pauli) paramagnetism whereas an additional temperature-dependent paramagnetic component is found in the Ru-rich region.

  9. Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Fujino, Aiko; Fukushima, Kei; Kubota, Takaharu; Kosugi, Tomomi; Takimoto-Kamimura, Midori, E-mail: m.kamimura@teijin.co.jp [Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512 (Japan)

    2013-11-01

    The Gly-rich loop of cyclin-dependent kinase 2 (CDK2) bound to TEI-I01800 as an MK2 specific inhibitor forms a β-sheet which is a common structure in CDK2–ligand complexes. Here, the reason why TEI-I01800 does not become a strong inhibitor against CDK2 based on the conformation of TEI-I01800 is presented. Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the MK2–TEI-I01800 complex has been reported; its Gly-rich loop was found to form an α-helix, not a β-sheet as has been observed for other Ser/Thr kinases. TEI-I01800 is 177-fold selective against MK2 compared with CDK2; in order to understand the inhibitory mechanism of TEI-I01800, the cyclin-dependent kinase 2 (CDK2) complex structure with TEI-I01800 was determined at 2.0 Å resolution. Interestingly, the Gly-rich loop of CDK2 formed a β-sheet that was different from that of MK2. In MK2, TEI-I01800 changed the secondary structure of the Gly-rich loop from a β-sheet to an α-helix by collision between Leu70 and a p-ethoxyphenyl group at the 7-position and bound to MK2. However, for CDK2, TEI-I01800 bound to CDK2 without this structural change and lost the interaction with the substituent at the 7-position. In summary, the results of this study suggest that the reason for the selectivity of TEI-I01800 is the favourable conformation of TEI-I01800 itself, making it suitable for binding to the α-form MK2.

  10. Free-standing nanomechanical and nanophotonic structures in single-crystal diamond

    Science.gov (United States)

    Burek, Michael John

    Realizing complex three-dimensional structures in a range of material systems is critical to a variety of emerging nanotechnologies. This is particularly true of nanomechanical and nanophotonic systems, both relying on free-standing small-scale components. In the case of nanomechanics, necessary mechanical degrees of freedom require physically isolated structures, such as suspended beams, cantilevers, and membranes. For nanophotonics, elements like waveguides and photonic crystal cavities rely on light confinement provided by total internal reflection or distributed Bragg reflection, both of which require refractive index contrast between the device and surrounding medium (often air). Such suspended nanostructures are typically fabricated in a heterolayer structure, comprising of device (top) and sacrificial (middle) layers supported by a substrate (bottom), using standard surface nanomachining techniques. A selective, isotropic etch is then used to remove the sacrificial layer, resulting in free-standing devices. While high-quality, crystalline, thin film heterolayer structures are readily available for silicon (as silicon-on-insulator (SOI)) or III-V semiconductors (i.e. GaAs/AlGaAs), there remains an extensive list of materials with attractive electro-optic, piezoelectric, quantum optical, and other properties for which high quality single-crystal thin film heterolayer structures are not available. These include complex metal oxides like lithium niobate (LiNbO3), silicon-based compounds such as silicon carbide (SiC), III-V nitrides including gallium nitride (GaN), and inert single-crystals such as diamond. Diamond is especially attractive for a variety of nanoscale technologies due to its exceptional physical and chemical properties, including high mechanical hardness, stiffness, and thermal conductivity. Optically, it is transparent over a wide wavelength range (from 220 nm to the far infrared), has a high refractive index (n ~ 2.4), and is host to a vast

  11. Crystal structure of the RNase T1 Gp c U complex

    International Nuclear Information System (INIS)

    Arni, R.K.

    1996-01-01

    Full text. Ribonuclease T 1 (RNase T 1 ; EC 3.1.27.3) a member of an extensive gene family of orthologous enzymes from fungi and bacteria that display sequence and structural homology. RNase T 1 is a guanine specific extracellular enzyme from Aspergillus oryzae that cleaves single stranded RNA by catalytic transesterification of 3,5 diester links to 2,3 cyclic diesters at guanylyl residues followed by their catalytic hydrolysis to corresponding 3 monoester. It has been suggested that subsites at both the 5 and 3 sides of a cleavable guanylyl residue in RNA substrates exist. The structure of the monomeric RNase T 1 2 guanosine mono phosphate was determined at 1.9 A resolution using syncrotron radiation (Arni et al. 1987) and revealed the specific interactions at the base recognition and catalytic sites (Arni et al., 1988). The structure of native RNase T 1 indicated the conformational changes of the amino acids forming the base recognition site (Arni et al., 1992). This protein has now been crystallized with Gpc U (Guanylyl (3,6) 6 deoxyhomouridine) which is an isosteric phosphonate analogue of the RNA fragment GpU (Guanylyl (3,5) Uridine), with the 5 oxygen of the uridine moiety replaced by a methylene. The structure has been determined and refined at 2.0 A resolution and indicates the existence of subsites and a novel ribose interaction. (author)

  12. Crystal structures of PRK1 in complex with the clinical compounds lestaurtinib and tofacitinib reveal ligand induced conformational changes.

    Directory of Open Access Journals (Sweden)

    Philip Chamberlain

    Full Text Available Protein kinase C related kinase 1 (PRK1 is a component of Rho-GTPase, androgen receptor, histone demethylase and histone deacetylase signaling pathways implicated in prostate and ovarian cancer. Herein we describe the crystal structure of PRK1 in apo form, and also in complex with a panel of literature inhibitors including the clinical candidates lestaurtinib and tofacitinib, as well as the staurosporine analog Ro-31-8220. PRK1 is a member of the AGC-kinase class, and as such exhibits the characteristic regulatory sequence at the C-terminus of the catalytic domain--the 'C-tail'. The C-tail fully encircles the catalytic domain placing a phenylalanine in the ATP-binding site. Our inhibitor structures include examples of molecules which both interact with, and displace the C-tail from the active site. This information may assist in the design of inhibitors targeting both PRK and other members of the AGC kinase family.

  13. Synthesis, properties, and crystal structure of complex Cp2Yb(DAD)

    International Nuclear Information System (INIS)

    Trifonov, A.A.; Kirillov, E.N.; Bochkarev, M.N.; Shumani, G.; Myule, S.

    1999-01-01

    Diazadiene complex of trivalent ytterbium Cp 2 Yb(DAD) (1) (DAD = Bu 1 -N CH-CH = N-Bu 1 ) was obtained by three routes: the oxidation of Cp 2 Yb(THF) 2 by diazadiene in tetrahydrofuran (THF), the reaction of Cp 2 YbCl with DAD 2- Na 2 + (2:1), and the reaction of Cp 2 YbCl(THF) with DAD - K + in the 1:1 ratio. Complex 1 was characterized by microanalysis, IR spectroscopy, magnetochemistry, and X-ray structural analysis [ru

  14. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

    Horak, Peter; Dantan, Aurelien Romain; Drewsen, Michael

    2012-01-01

    We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures, such as b......We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures...

  15. Synthesis, solvatochromism and crystal structure of trans-[Cu(Et2NCH2CH2NH2)2.H2O](NO3)2 complex: Experimental with DFT combination

    Science.gov (United States)

    Warad, Ismail; Musameh, Sharif; Badran, Ismail; Nassar, Nashaat N.; Brandao, Paula; Tavares, Carlos Jose; Barakat, Assem

    2017-11-01

    In this study, two dicationic asymmetrical diamine/copper(II) nitrate salt complexes of the general formula trans-[CuII(NN‧)2.H2O](NO3)2 were successfully synthesized using N,N-dimethylethylenediamine and N,N-diethylethylenediamine as asymmetrical diamine ligands. The structure of complex 2 was identified by X-ray single crystal diffraction analysis confirming that the bidentate ligand N,N-dimethylethylenediamine forms a penta-coordinated complex with an H2O molecule located around the copper(II) ion in a trans configuration. It was found that the metal centre is coordinated in a distorted square pyramidal fashion with a τ value of 0.274. The desired complexes were fully characterized using, MS, UV-Vis, CV, FTIR, TG/DTA, and Hirshfeld surface computational analysis. High level theoretical calculations were also performed in order to investigate the complexes structure, conformers, vibrational frequencies, and their excited states.

  16. Hydrogen-related complexes in Li-diffused ZnO single crystals

    Science.gov (United States)

    Corolewski, Caleb D.; Parmar, Narendra S.; Lynn, Kelvin G.; McCluskey, Matthew D.

    2016-07-01

    Zinc oxide (ZnO) is a wide band gap semiconductor and a potential candidate for next generation white solid state lighting applications. In this work, hydrogen-related complexes in lithium diffused ZnO single crystals were studied. In addition to the well-known Li-OH complex, several other hydrogen defects were observed. When a mixture of Li2O and ZnO is used as the dopant source, zinc vacancies are suppressed and the bulk Li concentration is very high (>1019 cm-3). In that case, the predominant hydrogen complex has a vibrational frequency of 3677 cm-1, attributed to surface O-H species. When Li2CO3 is used, a structured blue luminescence band and O-H mode at 3327 cm-1 are observed at 10 K. These observations, along with positron annihilation measurements, suggest a zinc vacancy-hydrogen complex, with an acceptor level ˜0.3 eV above the valence-band maximum. This relatively shallow acceptor could be beneficial for p-type ZnO.

  17. Hydrogen-related complexes in Li-diffused ZnO single crystals

    International Nuclear Information System (INIS)

    Corolewski, Caleb D.; Parmar, Narendra S.; Lynn, Kelvin G.; McCluskey, Matthew D.

    2016-01-01

    Zinc oxide (ZnO) is a wide band gap semiconductor and a potential candidate for next generation white solid state lighting applications. In this work, hydrogen-related complexes in lithium diffused ZnO single crystals were studied. In addition to the well-known Li-OH complex, several other hydrogen defects were observed. When a mixture of Li_2O and ZnO is used as the dopant source, zinc vacancies are suppressed and the bulk Li concentration is very high (>10"1"9" cm"−"3). In that case, the predominant hydrogen complex has a vibrational frequency of 3677 cm"−"1, attributed to surface O-H species. When Li_2CO_3 is used, a structured blue luminescence band and O-H mode at 3327 cm"−"1 are observed at 10 K. These observations, along with positron annihilation measurements, suggest a zinc vacancy–hydrogen complex, with an acceptor level ∼0.3 eV above the valence-band maximum. This relatively shallow acceptor could be beneficial for p-type ZnO.

  18. Crystal structure of the G3BP2 NTF2-like domain in complex with a canonical FGDF motif peptide.

    Science.gov (United States)

    Kristensen, Ole

    2015-11-06

    The crystal structure of the NTF2-like domain of the human Ras GTPase SH3 Binding Protein (G3BP), isoform 2, was determined at a resolution of 2.75 Å in complex with a peptide containing a FGDF sequence motif. The overall structure of the protein is highly similar to the homodimeric N-terminal domains of the G3BP1 and Rasputin proteins. Recently, a subset of G3BP interacting proteins was recognized to share a common sequence motif, FGDF. The most studied binding partners, USP10 and viral nsP3, interfere with essential G3BP functions related to assembly of cellular stress granules. Reported molecular modeling suggested that FGDF-motif containing peptides bind in an extended conformation into a hydrophobic groove on the surface of the G3BP NTF2-like domain in a manner similar to the known binding of FxFG nucleoporin repeats. The results in this paper provide evidence for a different binding mode. The FGDF peptide binds and changes conformation of the protruding N-terminal residues by providing hydrophobic interactions to a symmetry related molecule that facilitated crystallization of the G3BP2 isoform. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Synthesis and crystal structure of rare earth complexes with o-nitrobenzoic acid and N, N-dimethylformamide

    Science.gov (United States)

    Zhao, Lifang; Chen, Yashao; Bao, Lin

    2010-03-01

    The rare-earth compound [Ce 0.5Sm 0.5( o-NBA) 3(DMF) 2] 2 (where o-NBA = o-nitrobenzoic acid, DMF = N, N-dimethylformamide) has been synthesized and structurally characterized. The crystal structure of the compound is characterized by Fourier transfer infrared spectroscopy (FT-IR), fluorescent emission spectroscopy (FES) and single-crystal X-ray diffraction. The results show that the compound crystallizes in a triclinic system, space group P-1 with a = 11.8284 (6) Å, b = 12.5082 (7) Å, c = 13.0203 (7) Å, α = 63.9650 (10)°, β = 66.3900 (10)°, γ = 71.7380 (10)°, V = 1563.7 (14) Å 3, Dc = 1.677 g/cm 3, Z = 1, F(0 0 0) = 790. Each Ln (III) atom is bridged by four o-nitro-benzoates and chelated by one o-nitrobenzoate. The Ln (III) atom is eight-coordinated by six oxygen atoms from five o-nitro-benzoates and two oxygen atoms from two DMF molecules. Hydrogen bonds and aromatic π⋯ π stacking interactions assemble the compound into a three-dimensional network. Luminescence measurement shows that the compound emits fluorescence.

  20. Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

    Energy Technology Data Exchange (ETDEWEB)

    Cappadocia, Laurent; Maréchal, Alexandre; Parent, Jean-Sébastien; Lepage, Étienne; Sygusch, Jurgen; Brisson, Normand (Montreal)

    2010-09-07

    DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.

  1. Effect of preparation processes and structural insight into the supermolecular system: Bisacodyl and β-cyclodextrin inclusion complex

    International Nuclear Information System (INIS)

    Li, Shanshan; Zhai, Yuanming; Yan, Jin; Wang, Lili; Xu, Kailin; Li, Hui

    2016-01-01

    In this study, β-cyclodextrin (β-CD) and bisacodyl were chosen as model host and guest molecule to explore the effect of preparation processes on the physicochemical properties of inclusion complexes (ICs) and to gain an insight into the structure of ICs. The influence of temperature and pH on complexation was studied by multiple temperature–pH phase solubility analysis. The most favorable conformation was predicted by molecular modeling using AutoDock. "1H nuclear magnetic resonance and rotating frame nuclear Overhauser effect spectroscopy further confirmed the structure. Moreover, bisacodyl·β-CD ICs in solid state were successfully prepared via three different procedures (co-crystallization, co-evaporation, and co-grinding) and fully characterized by several solid-state techniques, namely, Fourier transform infrared spectroscopy, X-ray powder diffraction, thermogravimetric analysis, differential scanning calorimetry, solid-state NMR spectroscopy, and scanning electron microscopy. It was found that acid solution and low temperature were unfavorable for formation of bisacodyl·β-CD. The pyridine moiety was suggested to be enclosed in the hydrophobic cavity of β-CD. The complexes prepared using co-crystallization showed properties similar to those prepared using co-evaporation. Moreover, ICs obtained by co-evaporation and co-grinding had higher loading efficiency, water solubility, and dissolution rate than ICs obtained by co-crystallization. - Highlights: • The structure of inclusion complex-bisacodyl·β-CD was determined. • Thermodynamic behaviors of complexation under different conditions were discussed. • Products from three different preparation methods were systemically compared. • Co-crystallization and co-evaporation produced similar complexes. • Co-evaporation and co-grinding had better effects than co-crystallization.

  2. Effect of preparation processes and structural insight into the supermolecular system: Bisacodyl and β-cyclodextrin inclusion complex

    Energy Technology Data Exchange (ETDEWEB)

    Li, Shanshan [College of Chemical Engineering, Sichuan University, Chengdu 610065 (China); Zhai, Yuanming [Analytical and Testing Center, Sichuan University, Chengdu 610064 (China); Yan, Jin; Wang, Lili; Xu, Kailin [College of Chemical Engineering, Sichuan University, Chengdu 610065 (China); Li, Hui, E-mail: lihuilab@sina.com [College of Chemical Engineering, Sichuan University, Chengdu 610065 (China)

    2016-01-01

    In this study, β-cyclodextrin (β-CD) and bisacodyl were chosen as model host and guest molecule to explore the effect of preparation processes on the physicochemical properties of inclusion complexes (ICs) and to gain an insight into the structure of ICs. The influence of temperature and pH on complexation was studied by multiple temperature–pH phase solubility analysis. The most favorable conformation was predicted by molecular modeling using AutoDock. {sup 1}H nuclear magnetic resonance and rotating frame nuclear Overhauser effect spectroscopy further confirmed the structure. Moreover, bisacodyl·β-CD ICs in solid state were successfully prepared via three different procedures (co-crystallization, co-evaporation, and co-grinding) and fully characterized by several solid-state techniques, namely, Fourier transform infrared spectroscopy, X-ray powder diffraction, thermogravimetric analysis, differential scanning calorimetry, solid-state NMR spectroscopy, and scanning electron microscopy. It was found that acid solution and low temperature were unfavorable for formation of bisacodyl·β-CD. The pyridine moiety was suggested to be enclosed in the hydrophobic cavity of β-CD. The complexes prepared using co-crystallization showed properties similar to those prepared using co-evaporation. Moreover, ICs obtained by co-evaporation and co-grinding had higher loading efficiency, water solubility, and dissolution rate than ICs obtained by co-crystallization. - Highlights: • The structure of inclusion complex-bisacodyl·β-CD was determined. • Thermodynamic behaviors of complexation under different conditions were discussed. • Products from three different preparation methods were systemically compared. • Co-crystallization and co-evaporation produced similar complexes. • Co-evaporation and co-grinding had better effects than co-crystallization.

  3. Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A

    International Nuclear Information System (INIS)

    Mimasu, Shinya; Sengoku, Toru; Fukuzawa, Seketsu; Umehara, Takashi; Yokoyama, Shigeyuki

    2008-01-01

    Transcriptional activity and chromatin structure accessibility are correlated with the methylation of specific histone residues. Lysine-specific demethylase 1 (LSD1) is the first discovered histone demethylase, which demethylates Lys4 or Lys9 of histone H3, using FAD. Among the known monoamine oxidase inhibitors, tranylcypromine (Parnate) showed the most potent inhibitory effect on LSD1. Recently, the crystal structure of LSD1 and tranylcypromine was solved at 2.75 A, revealing a five-membered ring fused to the flavin of LSD1. In this study, we refined the crystal structure of the LSD1-tranylcypromine complex to 2.25 A. The five-membered ring model did not fit completely with the electron density, giving R work /R free values of 0.226/0.254. On the other hand, the N(5) adduct gave the lowest R work /R free values of 0.218/0.248, among the tested models. These results imply that the LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate, such as the N(5) adduct

  4. Solid-state dynamics and single-crystal to single-crystal structural transformations in octakis(3-chloropropyl)octasilsesquioxane and octavinyloctasilsesquioxane.

    Science.gov (United States)

    Kowalewska, A; Nowacka, M; Włodarska, M; Zgardzińska, B; Zaleski, R; Oszajca, M; Krajenta, J; Kaźmierski, S

    2017-10-18

    Reactive octahedral silsesquioxanes of rod-like [octakis(3-chloropropyl)octasilsesquioxane - T 8 (CH 2 CH 2 CH 2 Cl) 8 ] and spherical [octavinyloctasilsesquioxane - T 8 (CH[double bond, length as m-dash]CH 2 ) 8 ] structure can undergo reversible thermally induced phase transitions in the solid state. The phase behaviour has been studied with differential scanning calorimetry (DSC, including temperature modulated DSC), X-ray diffraction, dielectric relaxation spectroscopy (DRS), and nuclear magnetic resonance spectroscopy in the solid state (SS NMR), as well as positron annihilation lifetime spectroscopy (PALS) and polarized optical microscopy (POM). The mechanisms involving fitting the molecules into most symmetrical crystal lattices vary for species of different structure. Thermal energy can be used to expand the crystal lattice leading to thermochromism in the case of T 8 (CH[double bond, length as m-dash]CH 2 ) 8 or conversely to an unusual negative thermal expansion of crystals of T 8 (CH 2 CH 2 CH 2 Cl) 8 that results in their self-actuation. The complex behaviour is reflected in unusual changes in the capacitance and fractional free volume of the material. These phenomena can be used for molecular design of advanced well-defined hybrid materials capable of reversible thermally induced structural transformations. The findings present a new perspective for POSS-based flexible metal-organic frameworks (MOF) of cooperative structural transformability via entropy-based translational sub-net sliding.

  5. Crystal structure of core streptavidin determined from multi-wavelength anomalous diffraction of synchrotron radiation

    International Nuclear Information System (INIS)

    Hendrickson, W.A.; Paehler, A.; Smith, J.L.; Satow, Y.; Merritt, E.A.; Phizackerley, R.P.

    1989-01-01

    A three-dimensional crystal structure of the biotin-binding core of streptavidin has been determined at 3.1-angstrom resolution. The structure was analyzed from diffraction data measured at three wavelengths from a single crystal of the selenobiotinyl complex with streptavidin. Streptavidin is a tetramer with subunits arrayed in D 2 symmetry. Each protomer is an 8-stranded β-barrel with simple up-down topology. Biotin molecules are bound at one end of each barrel. This study demonstrates the effectiveness of multi-wavelength anomalous diffraction (MAD) procedures for macromolecular crystallography and provides a basis for detailed study of biotin-avidin interactions

  6. What makes a crystal structure report valid?

    NARCIS (Netherlands)

    Spek, Anthony L.|info:eu-repo/dai/nl/156517566

    2018-01-01

    Single crystal X-ray crystallography has developed into a unique, highly automated and accessible tool to obtain detailed information on molecular structures. Proper archival makes that referees, readers and users of the results of reported crystal structures no longer need to depend solely on the

  7. Preparation and crystal and molecular structure of tris(diethyldithiocarbamato)dimethylphenylphosphinetechnetium(III)

    International Nuclear Information System (INIS)

    Batsanov, A.S.; Struchkov, Yu.T.; Lorenz, B.; Wahren, M.

    1984-01-01

    The title compound Tc(S 2 CNEt 2 ) 3 (Me 2 PhP) I has been prepared by the reaction of TcCl 3 (Me 2 PhP) 3 with NaS 2 CNEt 2 . The crystal structure of I has been determined by single-crystal X-ray diffraction methods at room temperature. Crystals are rhombic, space group P2 1 2 1 2 1 , with a = 8.708(1), b = 12.012(1), c = 29.626(3) A and Z = 4. The compound consists of discrete I molecules. The technetium atom has a seven-coordinated environment which is best described as a distorted pentagonal bipyramid. The Tc-P distance (2.330(3) A) is remarkably short compared with other technetium complexes with mono-dentate phosphine ligands. (author)

  8. Determining Complex Structures using Docking Method with Single Particle Scattering Data

    Directory of Open Access Journals (Sweden)

    Haiguang Liu

    2017-04-01

    Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

  9. Synthesis, crystal structure determination of two-dimensional ...

    Indian Academy of Sciences (India)

    Abstract. The 2-D polymeric complex (I) has the formula [Ag(phSE)(NO3)]n, which has been crystallized from methanol-acetonitrile mixture and characterized by elemental analysis and single-crystal X-ray diffraction analysis. In this polymer, each Ag(I) ion occupies distorted trigonal pyramidal geometry coordinating with two.

  10. Microwave-Assisted Synthesis and Crystal Structure of Oxo(diperoxo(4,4'-di-tert-butyl-2,2'-bipyridine-molybdenum(VI

    Directory of Open Access Journals (Sweden)

    Alírio E. Rodrigues

    2009-09-01

    Full Text Available The oxodiperoxo complex MoO(O22(tbbpy (tbbpy = 4,4'-di-tert-butyl-2,2'- bipyridine was isolated from the reaction of MoO2Cl2(tbbpy in water under microwaveassisted heating at 120 ºC for 4 h. The structure of the oxodiperoxo complex was determined by single crystal X-ray diffraction. The MoVI centre is seven-coordinated with a geometry which strongly resembles a highly distorted bipyramid. Individual MoO(O22(tbbpy complexes are interdigitated along the [010] direction to form a column. The crystal structure is formed by the close packing of the columnar-stacked complexes. Interactions between neighbouring columns are essentially of van der Waals type mediated by the need to effectively fill the available space.

  11. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...

  12. Purification, crystallization and preliminary X-ray crystallographic analysis of the ETS domain of human Ergp55 in complex with the cfos promoter DNA sequence

    International Nuclear Information System (INIS)

    Gangwar, Shanti P.; Meena, Sita R.; Saxena, Ajay K.

    2012-01-01

    The ETS domain of human Ergp55 was purified and crystallized in native, complexes with E74, and cfos promoter DNA sequences. The X-ray intensity data set was collected on ETS–cfos promoter DNA complex crystal at 3.1 Å resolution to analyze the structure by molecular replacement technique. The Ergp55 protein belongs to the Ets family of transciption factors. The Ets transcription factors are involved in various developmental processes and the regulation of cancer metabolism. They contain a highly similar DNA-binding domain known as the ETS domain and have diverse functions in oncogenesis and physiology. The Ets transcription factors differ in their DNA-binding preference at the ETS site and the mechanisms by which they target genes are not clearly understood. To understand its DNA-binding mechanism, the ETS domain of Ergp55 was expressed and purified. The ETS domain was crystallized in the native form and in complex forms with DNA sequences from the E74 and cfos promoters. An X-ray diffraction data set was collected from an ETS–cfos DNA complex crystal at a wavelength of 0.9725 Å on the BM14 synchrotron beamline at the ESRF, France. The ETS–cfos DNA complex crystal belonged to space group C222 1 , with four molecules in the asymmetric unit. For structure analysis, initial phases for the ETS–cfos DNA complex were obtained by the molecular-replacement technique with Phaser in the CCP4 suite using the coordinates of Fli-1 protein and cfos DNA as search models. Structure analysis of the ETS–cfos DNA complex may possibly explain the DNA-binding specificity and its mechanism of interaction with the ETS domain of Ergp55

  13. Reactivity of Fe3(CO)12 with Alkynes R-C≡-C-R':Syntheses and Crystal Structures of Substituted Cyclic Ketones and Carbonyl Iron Complexes

    Institute of Scientific and Technical Information of China (English)

    SUO Quan-Ling; WU Le; SU Qian; ZHU Ning; GAO Yuan-Yuan; HONG Hai-Long; XIE Rui-Jun; HAN Li-Min

    2017-01-01

    The reactivity of carbonyl iron cluster with alkynes has been studied by the thermal reaction of Fe3(CO)12 with R-C≡C-R'(R =Fc (Ferrocenyl);R'=Ph (Phenyl),Fc,H).The hexacarbonyldiiron cluster with ferracyclopentadiene ring (μ2,η4-C4Ph4)Fe2(CO)6 (1) and one tetraphenyl substituted cyclopentadienone (Ph4C4CO) (2) were simultaneously obtained by the reaction of Fe3(CO)12 with alkyne (Ph-C≡C-Ph).Only one ferrole cluster (μ2,η4-C4Fc2H2)Fe2(CO)6 (3) was separated by using Fc-C≡C-H as alkyne.One tri-carbonyl iron complex (η4-C4Fc4CO)Fe(CO)3 (4) and an unexpected new cyclic ketone compound 2,2,4,5-tetraferrocenylcyclopenta-4-en-l,3-di-one [Fc4C3(CO)2] (5) were obtained by using Fc-C≡C-Fc as alkyne.A new complex (η4-2,4-diphenyl-3,5-diferrocenylcyclopenta-2,4-dien-l-one)-tricarbonyl iron (η4-C4Ph2Fc2CO)Fe(CO)3 (6)was synthesized by the reaction of Fe3(CO)12 with Fc-C≡C-Ph.The structures of compounds 1~6 were determined by X-ray single-crystal diffraction and spectroscopic characterization.The crystal structures of two new compounds 5 and 6 were analyzed.Our experimental results reveal the structural models of the reaction products are affected by the kinds of substituents from alkynes R-C≡C-R'.

  14. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

    Science.gov (United States)

    Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

    2015-10-01

    Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

  15. Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands

    International Nuclear Information System (INIS)

    Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S.; Damborsky, Jiri; Kuta Smatanova, Ivana

    2011-01-01

    Crystals of the wild-type haloalkane dehalogenase DhaA derived from R. rhodochrous NCIMB 13064 and of its catalytically inactive variant DhaA13 were grown in the presence of various ligands and diffraction data were collected to high and atomic resolution. Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon–halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2 1 2 1 2 1 as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively

  16. Structure of cadmium chloride complex with thiosemicarbazide Cd(NH2CSNHNH2)Cl2xH2O

    International Nuclear Information System (INIS)

    Gusev, A.I.; Chuklanova, E.B.; Murzubraimov, B.; Toktomamatov, A.

    1985-01-01

    The X-ray diffraction investigation of crystal and molecular structures of cadmium chloride complex with thiosemicarbaride is performed. Crystals are monoclinic with unit cell parameters: a=10.121(2), b=13.927(2), c=6.894(1) A, β=124.13(1) deg, Z=4, Cc sp. gr. The crystal structure consists of [Cd(NH 2 CSNHxNH 2 )Cl 2 ]n polymer chains and crystallization water molecules located between these chains. The cadmium coordination number equals 6, coordination polyhedron - tetragonal bipyramid

  17. Crystal structure refinement with SHELXL

    Energy Technology Data Exchange (ETDEWEB)

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  18. Two-dimensional photonic crystal accelerator structures

    Directory of Open Access Journals (Sweden)

    Benjamin M. Cowan

    2003-10-01

    Full Text Available Photonic crystals provide a method of confining a synchronous speed-of-light mode in an all-dielectric structure, likely a necessary feature in any optical accelerator. We explore computationally a class of photonic crystal structures with translational symmetry in a direction transverse to the electron beam. We demonstrate synchronous waveguide modes and discuss relevant parameters of such modes. We then explore how accelerator parameters vary as the geometry of the structure is changed and consider trade-offs inherent in the design of an accelerator of this type.

  19. Synthesis, spectroscopic, thermal and structural properties of 4-(2-aminoethyl)pyridinium tetracyanometallate(II) complexes

    Science.gov (United States)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

    2017-05-01

    In this study, three new complexes (4aepyH)2[Ni(CN)4] (1), (4aepyH)2[Pd(CN)4] (2) and (4aepyH)2[Pt(CN)4] (3) [4aepy = 4-(2-aminoethyl)pyridine] have been synthesized and characterized by elemental, thermal, vibrational (FT-IR and Raman) and single-crystal X-ray diffraction techniques. The crystallographic analyses reveal that the complexes crystallize in the monoclinic system, space group C2/c. The asymmetric units of the complexes contain one M(II) ion, two cyanide ligands and one non-coordinated the 4aepy ligand. Each M(II) ion is four coordinated with four cyanide-carbon atoms in a square planar geometry and the [M(CN)4]2- anions act as a counter ion. The 4aepyH cations in the complexes compose of the protonation of the 4aepy. The vibrational spectral data also supported to the crystal structures of the complexes. Thermal stabilities and decomposition products of the complexes were investigated in the temperature range 40-700 °C in the static air atmosphere.

  20. Synthesis, Crystal Structure and Water Vapor Adsorption Properties of a Porous Supramolecular Architecture

    Directory of Open Access Journals (Sweden)

    Rui Qiao

    2017-10-01

    Full Text Available A new complex, [Cu4(HL4(H2O14] (1, H3L·HCl = 5-((4-carboxypiperidin-1-ylmethylisophthalic acid hydrochloride, has been prepared and characterized by single-crystal X-ray diffraction, elemental analysis, IR spectroscopy and powder X-ray diffraction (PXRD. The result of the X-ray diffraction analysis reveals that the complex crystallizes in monoclinic, space group C2/c and three unique Cu(II atoms that are connected by partially deprotonated HL2− anion to form a cyclic structure. The rich hydrogen bonding and π-π non-covalent packing interactions extend cyclic units into a three-dimensional (3D supramolecular polymer. Moreover, the thermogravimetric (TG analysis and water vapor adsorption property of 1 were also discussed.

  1. Photonics of liquid-crystal structures: A review

    Energy Technology Data Exchange (ETDEWEB)

    Palto, S. P., E-mail: palto@online.ru; Blinov, L M; Barnik, M I; Lazarev, V V; Umanskii, B A; Shtykov, N M [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2011-07-15

    The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in detail. The formation of higher harmonics in the periodic distribution of the director field in a helical liquid crystal structure and, correspondingly, the new (anharmonic) mode of electro-optical effects are discussed. Another group of studies is devoted to bistable light switching by an electric field in chiral nematics. Polarization diffraction gratings controlled by an electric field are also considered. The results of studies devoted to microlasers on various photonic structures with cholesteric and nematic liquid crystals are considered in detail. Particular attention is given to the new regime: leaky-mode lasing. Designs of liquid crystal light amplifiers and their polarization, field, and spectral characteristics are considered in the last section.

  2. Synthesis, crystal growth and characterization of bioactive material: 2- Amino-1H-benzimidazolium pyridine-3-carboxylate single crystal- a proton transfer molecular complex

    Science.gov (United States)

    Fathima, K. Saiadali; Kavitha, P.; Anitha, K.

    2017-09-01

    The 1:1 molecular adducts 2- Amino-1H-benzimidazolium pyridine-3-carboxylate (2ABPC) was synthesized and grown as single crystal where 2-aminobenzimidazole (ABI) acts as a donor and nicotinic acid (NA) acts as an acceptor. The presence of proton and carbon were predicted using 1H and 13C NMR spectral analysis. The molecular structure of the crystal was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R = 0.038 for 2469 reflections. The vibrational modes of functional group have been studied using FTIR and Raman spectroscopic analysis. The UV-Vis spectrum exhibited a visible band at 246 nm for 2ABPC due to the nicotinate anion of the molecule. Further, the antimicrobial activity of 2ABPC complex against B. subtilis, klebsiella pneumonia, Pseudomonas eruginos and E. coli pathogens was investigated. Minimum Inhibitory Concentration (MIC) for this crystal was obtained using UV spectrometer against MRSA pathogen. It was found that the benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of 2ABPC crystal.

  3. Synthesis and Crystal Structure of Binuclear and Pentanuclear Nickel(II Complexes Containing 4-(salicylaldiminatoantipyrine Schiff base

    Directory of Open Access Journals (Sweden)

    Mohamed N. EL-Kaheli

    2015-11-01

    Full Text Available The new title binuclear Ni (II compound  (1 and the novel pentanuclear Ni (II cluster {[   } (2 are formed from the reaction of an asymmetric Schiff base ligand L (L = 4-(salicylaldiminatoantipyrine with Ni .4  in the former or Ni(ClO42.6H2O in presence of malonate in the later.  Complex (1 consists of ( ]+ cation and one uncoordinated tetraphenylborate anion.  The cation adopts a distorted octahedral arrangement around each metal center.  In the binuclear unit both Ni(II ions are linked through two phenolate (µ2-O oxygen atoms of L, and two oxygen atoms of a  bridging carboxylate group. Each Ni (II coordinates to four oxygen atoms at the basal plane, two oxygen atoms from two bridging phenolate groups, one from pyrazolone ring and the last of an aqua molecule, and at the axial positions to a bridging carboxylate-O atom and an azomethine nitrogen atom.  In the pentanuclear cluster (2 consisting of [ ]+2 cation and two tetraphenylborate anions, the core of the cation is assembled by four [Ni( ] units, linked to the central Ni-ion by two bridging water molecules. The resulting coordination sphere for the external symmetry related nickel ions is a pseudo octahedron.  The central Ni-atom unusually adopts dodecahedron geometry through its coordination to eight bridging water molecules. In complex (1 each Ni-atom is coordinated to one tridentate L ligand and in complex (2 each [Ni ( ] unit is coordinated to two bidentate L ligands.  Inter-and intramolecular hydrogen bonds are present in both crystal structures.

  4. Crystal structures and catalytic performance of three new methoxy substituted salen type nickel(II) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

    Science.gov (United States)

    Ghaffari, Abolfazl; Behzad, Mahdi; Pooyan, Mahsa; Amiri Rudbari, Hadi; Bruno, Giuseppe

    2014-04-01

    Three new nickel(II) complexes of a series of methoxy substituted salen type Schiff base ligands were synthesized and characterized by IR, UV-Vis and 1H NMR spectroscopy and elemental analysis. The ligands were synthesized from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with n-methoxysalicylaldehyde (n = 3, 4 and 5). Crystal structures of these complexes were determined. Electrochemical behavior of the complexes was studied by means of cyclic voltammetry in DMSO solutions. Catalytic performance of the complexes was studied in the epoxidation of cyclooctene using tert-butylhydroperoxide (TBHP) as oxidant under various conditions to find the optimum operating parameters. Low catalytic activity with moderate epoxide selectivity was observed in in-solvent conditions but in the solvent-free conditions, enhanced catalytic activity with high epoxide selectivity was achieved.

  5. Synthesis, crystal structure, and magnetic properties of two-dimensional divalent metal glutarate/dipyridylamine coordination polymers, with a single crystal-to-single crystal transformation in the copper derivative

    International Nuclear Information System (INIS)

    Montney, Matthew R.; Supkowski, Ronald M.; Staples, Richard J.; LaDuca, Robert L.

    2009-01-01

    Hydrothermal reaction of divalent metal chlorides with glutaric acid and 4,4'-dipyridylamine (dpa) has afforded an isostructural family of coordination polymers with formulation [M(glu)(dpa)] n (M=Co (1), Ni (2), Cu (3); glu=glutarate). Square pyramidal coordination is seen in 1-3, with semi-ligation of a sixth donor to produce a '5+1' extended coordination sphere. Neighboring metal atoms are linked into 1D [M(glu)] n neutral chains through chelating/monodentate bridging glutarate moieties with a syn-anti binding mode, and semi-chelation of the pendant carboxylate oxygen. These chains further connect into 2D layers through dipodal dpa ligands. Neighboring layers stack into the pseudo 3D crystal structure of 1-3 through supramolecular hydrogen bonding between dpa amine units and the semi-chelated glutarate oxygen atoms. The variable temperature magnetic behavior of 1-3 was explored and modeled as infinite 1D Heisenberg chains. Notably, complex 3 undergoes a thermally induced single crystal-to-single crystal transformation between centric and acentric space groups, with a conformationally disordered unilayer structure at 293 K and an ordered bilayer structure at 173 K. All materials were further characterized via infrared spectroscopy and elemental and thermogravimetric analyses. - Graphical abstract: The coordination polymers [M(glu)(dpa)] n (M=Co (1), Ni (2), Cu (3); glu=glutarate, dpa=4,4'-dipyridylamine) exhibit 2D layer structures based on 1D [M(glu)] n chains linked through dpa tethers. Antiferromagnetic coupling is observed for 2 and 3, while ferromagnetism is predominant in 1. Compound 3 undergoes a thermally induced single crystal-to-single crystal transformation from an acentric to a centrosymmetric space group

  6. Crystal structure of the NADP+ and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.

    Science.gov (United States)

    Yoneda, Kazunari; Sakuraba, Haruhiko; Araki, Tomohiro; Ohshima, Toshihisa

    2018-05-01

    A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C. The enzyme showed substantial reactivity towards D-serine, in addition to L-serine. Two different crystal structures of P. calidifontis L-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP + /sulfate ion at 1.18 Å and the structure in complex with NADP + /L-tartrate (substrate analog) at 1.57 Å. The fold of the catalytic domain showed similarity with that of Ps. aeruginosa L-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. This is the first description of the structure of the novel type of L-SerDH with bound NADP + and substrate analog, and it provides new insight into the substrate binding mechanism of L-SerDH. The results obtained here may be very informative for the creation of L- or D-serine-specific SerDH by protein engineering.

  7. THE STRUCTURE OF PHOTOSYSTEM-I FROM THE THERMOPHILIC CYANOBACTERIUM SYNECHOCOCCUS SP DETERMINED BY ELECTRON-MICROSCOPY OF 2-DIMENSIONAL CRYSTALS

    NARCIS (Netherlands)

    BOTTCHER, B; GRABER, P; BOEKEMA, EJ

    1992-01-01

    The structure of the Photosystem I (PS I) complex from the thermophilic cyanobacterium Synechococcus sp. has been investigated by electron microscopy and image analysis of two-dimensional crystals. Crystals were obtained from isolated PS I by removal of detergents with Bio-Beads. After negative

  8. Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p.

    Science.gov (United States)

    Koyama, Masako; Hirano, Hidemi; Shirai, Natsuki; Matsuura, Yoshiyuki

    2017-10-01

    Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine-glycine (so-called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif. The crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex identified three binding sites for the SxFG/PxFG repeats on HEAT repeats 14-20 of Xpo1p. Mutational analyses of Nup42p showed that the conserved serines and prolines in the SxFG/PxFG repeats contribute to Xpo1p-Nup42p binding. Our structural and biochemical data suggest that SxFG/PxFG-Nups such as Nup42p and Nup159p at the cytoplasmic face of NPCs provide high-affinity docking sites for the Xpo1p nuclear export complex in the terminal stage of NPC passage and that subsequent disassembly of the nuclear export complex facilitates recycling of free Xpo1p back to the nucleus. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  9. Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin.

    Science.gov (United States)

    Nakamura, Toshio; Kotani, Mao; Tonozuka, Takashi; Ide, Azusa; Oguma, Keiji; Nishikawa, Atsushi

    2009-01-30

    The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play an important role cooperatively with HA1 in the internalization of the toxin by gastrointestinal epithelial cells via binding of these subcomponents to specific oligosaccharides. In this study, we investigated the sugar-binding specificity of the HA3b subcomponent using recombinant protein fused to glutathione S-transferase and determined the three-dimensional structure of the HA3a-HA3b complex based on X-ray crystallography. The crystal structure was determined at a resolution of 2.6 A. HA3b contains three domains, domains I to III, and the structure of domain I resembles HA3a. In crystal packing, three HA3a-HA3b molecules are assembled to form a three-leaved propeller-like structure. The three HA3b domain I and three HA3a alternate, forming a trimer of dimers. In a database search, no proteins with high structural homology to any of the domains (Z score >10) were found. Especially, HA3a and HA3b domain I, mainly composed of beta-sheets, reveal a unique fold. In binding assays, HA3b bound sialic acid with high affinity, but did not bind galactose, N-acetylgalactosamine, or N-acetylglucosamine. The electron density of liganded N-acetylneuraminic acid was determined by crystal soaking. In the sugar-complex structure, the N-acetylneuraminic acid-binding site was located in the cleft formed between domains II and III of HA3b. This report provides the first determination of the three-dimensional structure of the HA3a-HA3b complex and its sialic acid binding site. Our results will provide useful information for elucidating the mechanism of assembly of the C16S toxin and for understanding the interactions with oligosaccharides on epithelial cells and internalization of the botulinum toxin complex.

  10. ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations

    Energy Technology Data Exchange (ETDEWEB)

    Burnett, M.N.; Johnson, C.K.

    1996-07-01

    This report describes a computer program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids on the atomic sites. The program can also produce stereoscopic pairs of illustrations which aid in the visualization of complex packing arrangements of atoms and thermal motion patterns. Interatomic distances, bond angles, and principal axes of thermal motion are also calculated to aid the structural study.

  11. The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution.

    OpenAIRE

    Czworkowski, J; Wang, J; Steitz, T A; Moore, P B

    1994-01-01

    Elongation factor G (EF-G) catalyzes the translocation step of protein synthesis in bacteria, and like the other bacterial elongation factor, EF-Tu--whose structure is already known--it is a member of the GTPase superfamily. We have determined the crystal structure of EF-G--GDP from Thermus thermophilus. It is an elongated molecule whose large, N-terminal domain resembles the G domain of EF-Tu, except for a 90 residue insert, which covers a surface that is involved in nucleotide exchange in E...

  12. Crystallization and preliminary X-ray diffraction analysis of mouse galectin-4 N-terminal carbohydrate recognition domain in complex with lactose

    International Nuclear Information System (INIS)

    Krejčiříková, Veronika; Fábry, Milan; Marková, Vladimíra; Malý, Petr; Řezáčová, Pavlína; Brynda, Jiří

    2008-01-01

    Mouse galectin-4 carbohydrate binding domain was overexpressed in E. coli and crystallized in the presence of lactose. The crystals belong to tetragonal space group P42 1 2 and diffraction data were collected to 2.1 Å resolution. Galectin-4 is thought to play a role in the process of tumour conversion of cells of the alimentary tract and the breast tissue; however, its exact function remains unknown. With the aim of elucidating the structural basis of mouse galectin-4 (mGal-4) binding specificity, we have undertaken X-ray analysis of the N-terminal domain, CRD1, of mGal-4 in complex with lactose (the basic building block of known galectin-4 carbohydrate ligands). Crystals of CRD1 in complex with lactose were obtained using vapour-diffusion techniques. The crystals belong to tetragonal space group P42 1 2 with unit-cell parameters a = 91.1, b = 91.16, c = 57.10 Å and preliminary X-ray diffraction data were collected to 3.2 Å resolution. An optimized crystallization procedure and cryocooling protocol allowed us to extend resolution to 2.1 Å. Structure refinement is currently under way; the initial electron-density maps clearly show non-protein electron density in the vicinity of the carbohydrate binding site, indicating the presence of one lactose molecule. The structure will help to improve understanding of the binding specificity and function of the potential colon cancer marker galectin-4

  13. Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1–RuvBL2 complex

    International Nuclear Information System (INIS)

    Gorynia, Sabine; Matias, Pedro M.; Bandeiras, Tiago M.; Donner, Peter; Carrondo, Maria Arménia

    2008-01-01

    A truncated variant of the human RuvBL1–RuvBL2 complex was cloned, expressed, purified and crystallised. Synchrotron diffraction data to 4 Å resolution were used to carry out a preliminary crystallographic analysis of the complex. The complex of RuvBL1 and its homologue RuvBL2, two evolutionarily highly conserved eukaryotic proteins belonging to the AAA + (ATPase associated with diverse cellular activities) family of ATPases, was co-expressed in Escherichia coli. For crystallization purposes, the flexible domains II of RuvBL1 and RuvBL2 were truncated. The truncated RuvBL1–RuvBL2 complex was crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystals were hexagonal-shaped plates and belonged to either the orthorhombic space group C222 1 , with unit-cell parameters a = 111.4, b = 188.0, c = 243.4 Å and six monomers in the asymmetric unit, or the monoclinic space group P2 1 , with unit-cell parameters a = 109.2, b = 243.4, c = 109.3 Å, β = 118.7° and 12 monomers in the asymmetric unit. The crystal structure could be solved by molecular replacement in both possible space groups and the solutions obtained showed that the complex forms a dodecamer

  14. Hydrogen-related complexes in Li-diffused ZnO single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Corolewski, Caleb D. [Materials Science and Engineering Program, Washington State University, Pullman, Washington 99164-2814 (United States); Parmar, Narendra S.; Lynn, Kelvin G. [Center for Materials Research, Washington State University, Pullman, Washington 99164-2814 (United States); McCluskey, Matthew D., E-mail: mattmcc@wsu.edu [Materials Science and Engineering Program, Washington State University, Pullman, Washington 99164-2814 (United States); Department of Physics and Astronomy, Washington State University, Pullman, Washington 99164-2814 (United States)

    2016-07-21

    Zinc oxide (ZnO) is a wide band gap semiconductor and a potential candidate for next generation white solid state lighting applications. In this work, hydrogen-related complexes in lithium diffused ZnO single crystals were studied. In addition to the well-known Li-OH complex, several other hydrogen defects were observed. When a mixture of Li{sub 2}O and ZnO is used as the dopant source, zinc vacancies are suppressed and the bulk Li concentration is very high (>10{sup 19 }cm{sup −3}). In that case, the predominant hydrogen complex has a vibrational frequency of 3677 cm{sup −1}, attributed to surface O-H species. When Li{sub 2}CO{sub 3} is used, a structured blue luminescence band and O-H mode at 3327 cm{sup −1} are observed at 10 K. These observations, along with positron annihilation measurements, suggest a zinc vacancy–hydrogen complex, with an acceptor level ∼0.3 eV above the valence-band maximum. This relatively shallow acceptor could be beneficial for p-type ZnO.

  15. Comparison of multiple crystal structures with NMR data for engrailed homeodomain

    Energy Technology Data Exchange (ETDEWEB)

    Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

    2008-03-15

    Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

  16. Pyrazole complexes of rhenium. Synthesis and crystal structure of trans-[Re(O)(OMe)L4]Br2 · L · 4H2O (L - 3,5-dimethylpyrazole)

    International Nuclear Information System (INIS)

    Sokolov, M.N.; Fedorova, N.Eh.; Fedorov, V.E.; Virovets, A.V.; Nun'es, P.

    2002-01-01

    The first rhenium (V) mononuclear complex featuring composition [Re(O)(OMe)L 4 ]Br 2 (L = 3,5-dimethylpyrazole), which is resistant to hydrolysis in neutral aqueous solution, along with its molecular adduct of the composition [Re(O)(OMe)L 4 ]Br 2 · L · 4H 2 O were synthesized. The reaction products were characterized by the methods of elementary analysis, absorption spectroscopy in visible, UV and IR ranges, mass spectrometry. Besides, the adduct structure was studied by the method of X-ray diffraction analysis. It was ascertained that the adduct is crystallized in tetragonal crystal system with unit cell parameters as follows: a = 14.912 (3), c = 17.108 (4) A, sp. gr. I4/m, Z = 4. In the complex molecule linear grouping Re(O)(OMe)] 2+ (Re-O-C angle being equal to 180 deg) is coordinated by four L ligand molecules [ru

  17. SYNTHESIS, CRYSTAL STRUCTURE AND MAGNETIC ...

    African Journals Online (AJOL)

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    Much of the current effort on such extended hybrid metal organic complexes is ... In this paper, we report the synthesis, single crystal X-ray diffraction analysis and ..... with g = 2.0 (0.37 cm3 mol−1 K), and smoothly increases to a value of 0.45 ...

  18. Crystal Structure of an LSD-Bound Human Serotonin Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D.; Betz, Robin M.; Venkatakrishnan, A.J.; Levit, Anat; Lansu, Katherine; Schools, Zachary L.; Che, Tao; Nichols, David E.; Shoichet, Brian K.; Dror, Ron O.; Roth, Bryan L. (UNCSM); (UNC); (Stanford); (Stanford-MED); (UCSF)

    2017-01-01

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.

  19. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  20. Crystal Structure of an LSD-Bound Human Serotonin Receptor.

    Science.gov (United States)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D; Betz, Robin M; Venkatakrishnan, A J; Levit, Anat; Lansu, Katherine; Schools, Zachary L; Che, Tao; Nichols, David E; Shoichet, Brian K; Dror, Ron O; Roth, Bryan L

    2017-01-26

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT 2B . The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT 2B R and 5-HT 2A R-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Preparation and crystallization of the Grb7 SH2 domain in complex with the G7-18NATE nonphosphorylated cyclic inhibitor peptide

    International Nuclear Information System (INIS)

    Yap, Min Y.; Wilce, Matthew C. J.; Clayton, Daniel J.; Perlmutter, Patrick; Aguilar, Marie-Isabel; Wilce, Jacqueline A.

    2010-01-01

    The preparation and successful crystallization of the Grb7 SH2 domain in complex with the specific cyclic peptide inhibitor G7-18NATE are reported. This structure is anticipated to reveal the basis of the binding affinity and specificity and to assist with the development of second-generation inhibitors of Grb7, which is involved in cancer progression. Grb7 is an adapter protein that is involved in signalling pathways that mediate eukaryotic cell proliferation and migration. Its overexpression in several cancer types has implicated it in cancer progression and led to the development of the G7-18NATE cyclic peptide inhibitor. Here, the preparation of crystals of G7-18NATE in complex with its Grb7 SH2 domain target is reported. Crystals of the complex were grown by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant at room temperature. X-ray diffraction data were collected from crystals to 2.4 Å resolution using synchrotron X-ray radiation at 100 K. The diffraction was consistent with space group P2 1 , with unit-cell parameters a = 52.7, b = 79.1, c = 54.7 Å, α = γ = 90.0, β = 104.4°. The structure of the G7-18NATE peptide in complex with its target will facilitate the rational development of Grb7-targeted cancer therapeutics

  2. Structure analysis on synthetic emerald crystals

    Science.gov (United States)

    Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

    2013-05-01

    Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

  3. Surface induces different crystal structures in a room temperature switchable spin crossover compound.

    Science.gov (United States)

    Gentili, Denis; Liscio, Fabiola; Demitri, Nicola; Schäfer, Bernhard; Borgatti, Francesco; Torelli, Piero; Gobaut, Benoit; Panaccione, Giancarlo; Rossi, Giorgio; Degli Esposti, Alessandra; Gazzano, Massimo; Milita, Silvia; Bergenti, Ilaria; Ruani, Giampiero; Šalitroš, Ivan; Ruben, Mario; Cavallini, Massimiliano

    2016-01-07

    We investigated the influence of surfaces in the formation of different crystal structures of a spin crossover compound, namely [Fe(L)2] (LH: (2-(pyrazol-1-yl)-6-(1H-tetrazol-5-yl)pyridine), which is a neutral compound thermally switchable around room temperature. We observed that the surface induces the formation of two different crystal structures, which exhibit opposite spin transitions, i.e. on heating them up to the transition temperature, one polymorph switches from high spin to low spin and the second polymorph switches irreversibly from low spin to high spin. We attributed this inversion to the presence of water molecules H-bonded to the complex tetrazolyl moieties in the crystals. Thin deposits were investigated by means of polarized optical microscopy, atomic force microscopy, X-ray diffraction, X-ray absorption spectroscopy and micro Raman spectroscopy; moreover the analysis of the Raman spectra and the interpretation of spin inversion were supported by DFT calculations.

  4. Nonlinear effects at volume charge polarization and calculation of the structure radiation changes in the crystals with hydrogen bonds

    International Nuclear Information System (INIS)

    Tonkonogov, M.P.; Medvedev, V.Ya.

    2003-01-01

    The formulas for volume charge distribution, complex permittivity, static dielectric constant for the crystals with hydrogen bonds are proposed. With help of the formulas the structure defect concentration, relaxation energy of relaxators were calculated for important electronic and optoelectronic materials as mica, KDP and DKDP crystals, gypsum, talk

  5. Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex.

    Science.gov (United States)

    Jaiswal, Rahul; Singh, Samarendra K; Bastia, Deepak; Escalante, Carlos R

    2015-04-01

    The Reb1 protein from Schizosaccharomyces pombe is a member of a family of proteins that control programmed replication termination and/or transcription termination in eukaryotic cells. These events occur at naturally occurring replication fork barriers (RFBs), where Reb1 binds to termination (Ter) DNA sites and coordinates the polar arrest of replication forks and transcription approaching in opposite directions. The Reb1 DNA-binding and replication-termination domain was expressed in Escherichia coli, purified and crystallized in complex with a 26-mer DNA Ter site. Batch crystallization under oil was required to produce crystals of good quality for data collection. Crystals grew in space group P2₁, with unit-cell parameters a = 68.9, b = 162.9, c = 71.1 Å, β = 94.7°. The crystals diffracted to a resolution of 3.0 Å. The crystals were mosaic and required two or three cycles of annealing. This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination.

  6. Synthesis and crystal structure of a new homoleptic tetraarylruthenium(IV) complex Ru(2,4,5-Me{sub 3}C{sub 6}H{sub 2}){sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chang-Jiu; Wu, Xiu-Li; Ma, Xiu-Fang; Jia, Ai-Quan; Zhang, Qian-Feng [Anhui Univ. of Technology, Anhui (China). Inst. of Molecular Engineering and Applied Chemistry and Anhui Province Key Lab. of Metallurgy Engineering and Resources Recycling

    2017-08-01

    Treatment of [Ru(acac){sub 3}] (acac-=acetylacetonate) with (2,4,5-Me{sub 3}C{sub 6}H{sub 2})MgBr, followed by column chromatography in air, afforded the homoleptic tetraaryl-ruthenium(IV) complex [Ru(2,4,5-Me{sub 3}C{sub 6}H{sub 2}){sub 4}] (1) in moderate yield. The product was characterized by proton NMR spectroscopy and microanalyses. Its crystal structure has also been established by X-ray crystallography.

  7. Glycine Betaine Recognition through Cation−π Interactions in Crystal Structures of Glycine Betaine Complexes with C-Ethyl-pyrogallol[4]arene and C-Ethyl-resorcin[4]arene as Receptors

    Directory of Open Access Journals (Sweden)

    Ikuhide Fujisawa

    2013-04-01

    Full Text Available The glycine betaine (betaine, interacts with several types of proteins with diverse structures in vivo, and in the contact regions, the aromatic rings of protein residues are frequently found beside the trimethylammonium group of betaine, implying the importance of the cation−π interactions in recognition of this molecule. The crystal structures determined by X-ray crystallography of the complexes of betaine and C-ethyl-pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT and betaine and C-ethyl-resorcin[4]arene (resorcinol cyclic tetramer: RCT mimic the conformations of betaine and protein complexes and show that the clathrate conformations are retained by the cation−π interactions. The difference of the conformation feature of betaine in the Protein Data Bank and in the Cambridge Structural Database was found by chance during the research and analyzed with the torsion angles.

  8. Crystal structure of the[mu]-opioid receptor bound to a morphinan antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Mathiesen, Jesper M.; Sunahara, Roger K.; Pardo, Leonardo; Weis, William I.; Kobilka, Brian K.; Granier, Sébastien (Michigan-Med); (Stanford-MED); (UAB, Spain)

    2012-06-27

    Opium is one of the world's oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnoea and dependence) by binding to and activating the G-protein-coupled {mu}-opioid receptor ({mu}-OR) in the central nervous system. Here we describe the 2.8 {angstrom} crystal structure of the mouse {mu}-OR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket observed in most G-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the {mu}-OR crystallizes as a two-fold symmetrical dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.

  9. Studies on growth, crystal structure and characterization of novel organic nicotinium trifluoroacetate single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Dhanaraj, P.V. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Rajesh, N.P., E-mail: rajeshnp@hotmail.com [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Sundar, J. Kalyana; Natarajan, S. [Department of Physics, Madurai Kamaraj University, Madurai 625 021 (India); Vinitha, G. [Department of Physics, Crescent Engineering College, Chennai 600 048 (India)

    2011-09-15

    Highlights: {yields} Good quality crystals of nicotinium trifluoroacetate in monoclinic system were grown for first time. {yields} Nicotinium trifluoroacetate crystal exhibits third order nonlinear optical properties. {yields} The optical spectrum of nicotinium trifluoroacetate crystal reveals the wide transmission in the entire range with cutoff wavelength at 286 nm. {yields} Nicotinium trifluoroacetate is a low dielectric constant material. - Abstract: An organic material, nicotinium trifluoroacetate (NTF) was synthesized and single crystals in monoclinic system were grown from aqueous solution for the first time. Its solubility and metastable zone width were estimated. The crystal structure of NTF was analyzed to reveal the molecular arrangements and the formation of hydrogen bonds in the crystal. High-resolution X-ray diffraction rocking curve measurements were performed to analyze the structural perfection of the grown crystals. Functional groups in NTF were identified by Fourier transform infrared spectral analysis. Thermal behaviour and stability of NTF were studied by thermogravimetric and differential thermal analysis and differential scanning calorimetry. Mechanical and dielectric properties of NTF crystals were analyzed. Optical studies reveal that NTF crystals are transparent in the wavelength range 286-1100 nm. The third order nonlinear optical parameters of NTF were derived by the Z-scan technique.

  10. Cloud chamber experiments on the origin of ice crystal complexity in cirrus clouds

    Directory of Open Access Journals (Sweden)

    M. Schnaiter

    2016-04-01

    Full Text Available This study reports on the origin of small-scale ice crystal complexity and its influence on the angular light scattering properties of cirrus clouds. Cloud simulation experiments were conducted at the AIDA (Aerosol Interactions and Dynamics in the Atmosphere cloud chamber of the Karlsruhe Institute of Technology (KIT. A new experimental procedure was applied to grow and sublimate ice particles at defined super- and subsaturated ice conditions and for temperatures in the −40 to −60 °C range. The experiments were performed for ice clouds generated via homogeneous and heterogeneous initial nucleation. Small-scale ice crystal complexity was deduced from measurements of spatially resolved single particle light scattering patterns by the latest version of the Small Ice Detector (SID-3. It was found that a high crystal complexity dominates the microphysics of the simulated clouds and the degree of this complexity is dependent on the available water vapor during the crystal growth. Indications were found that the small-scale crystal complexity is influenced by unfrozen H2SO4 / H2O residuals in the case of homogeneous initial ice nucleation. Angular light scattering functions of the simulated ice clouds were measured by the two currently available airborne polar nephelometers: the polar nephelometer (PN probe of Laboratoire de Métérologie et Physique (LaMP and the Particle Habit Imaging and Polar Scattering (PHIPS-HALO probe of KIT. The measured scattering functions are featureless and flat in the side and backward scattering directions. It was found that these functions have a rather low sensitivity to the small-scale crystal complexity for ice clouds that were grown under typical atmospheric conditions. These results have implications for the microphysical properties of cirrus clouds and for the radiative transfer through these clouds.

  11. Band structures in fractal grading porous phononic crystals

    Science.gov (United States)

    Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

    2018-05-01

    In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

  12. Construction of crystal structure prototype database: methods and applications.

    Science.gov (United States)

    Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

    2017-04-26

    Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

  13. Construction of crystal structure prototype database: methods and applications

    International Nuclear Information System (INIS)

    Su, Chuanxun; Lv, Jian; Wang, Hui; Wang, Yanchao; Ma, Yanming; Li, Quan; Zhang, Lijun

    2017-01-01

    Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery. (paper)

  14. Copper(II) and palladium(II) complexes with tridentate NSO donor Schiff base ligand: Synthesis, characterization and structures

    Science.gov (United States)

    Kumar, Sujit Baran; Solanki, Ankita; Kundu, Suman

    2017-09-01

    Mononuclear copper(II) complex [CuL2] and palladium(II) complexes [Pd(X)L] where X = benzoate(bz) or salicylate(sal) and HL = 2-(methylthio)phenylimino)methyl)phenol, a Schiff base ligand with NSO coordination sites have been synthesized and characterized by microanalyses, IR, UV-Visible spectra, conductivity measurement and magnetic studies. Crystal structures of all the complexes have been solved by single crystal X-ray diffraction studies and showed that there are two molecules in a unit cell in the [CuL2] complex - one molecule has square planar geometry whereas second molecule has distorted square pyramidal geometry and palladium(II) complexes have distorted square planar geometry.

  15. Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

    Science.gov (United States)

    Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

    2017-06-01

    We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

  16. Crystallization of Doc and the Phd-Doc toxin-antitoxin complex.

    Science.gov (United States)

    Garcia-Pino, Abel; Dao-Thi, Minh-Hoa; Gazit, Ehud; Magnuson, Roy David; Wyns, Lode; Loris, Remy

    2008-11-01

    The phd/doc addiction system is responsible for the stable inheritance of lysogenic bacteriophage P1 in its plasmidic form in Escherichia coli and is the archetype of a family of bacterial toxin-antitoxin modules. The His66Tyr mutant of Doc (Doc(H66Y)) was crystallized in space group P2(1), with unit-cell parameters a = 53.1, b = 198.0, c = 54.1 A, beta = 93.0 degrees . These crystals diffracted to 2.5 A resolution and probably contained four dimers of Doc in the asymmetric unit. Doc(H66Y) in complex with a 22-amino-acid C-terminal peptide of Phd (Phd(52-73Se)) was crystallized in space group C2, with unit-cell parameters a = 111.1, b = 38.6, c = 63.3 A, beta = 99.3 degrees , and diffracted to 1.9 A resolution. Crystals of the complete wild-type Phd-Doc complex belonged to space group P3(1)21 or P3(2)21, had an elongated unit cell with dimensions a = b = 48.9, c = 354.9 A and diffracted to 2.4 A resolution using synchrotron radiation.

  17. Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.

    Science.gov (United States)

    Handing, Katarzyna B; Shabalin, Ivan G; Szlachta, Karol; Majorek, Karolina A; Minor, Wladek

    2016-03-01

    Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1Å. Cetirizine is bound in two sites--a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizine binding sites. We show that the residues forming the binding pockets in ESA are highly conserved in human serum albumin (HSA), and suggest that binding of cetirizine to HSA will be similar. In support of that hypothesis, we show that the dissociation constants for cetirizine binding to CBS2 in ESA and HSA are identical using tryptophan fluorescence quenching. Presence of lysine and arginine residues that have been previously reported to undergo nonenzymatic glycosylation in CBS1 and CBS2 suggests that cetirizine transport in patients with diabetes could be altered. A review of all available SA structures from the PDB shows that in addition to the novel drug binding site we present here (CBS1), there are two pockets on SA capable of binding drugs that do not overlap with fatty acid binding sites and have not been discussed in published reviews. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Crystal structure study of new lanthanide silicates with silico-carnotite structure

    International Nuclear Information System (INIS)

    Piccinelli, F.; Lausi, A.; Speghini, A.; Bettinelli, M.

    2012-01-01

    The crystal structures of new rare earth-based silicate compounds (Ca 3 Eu 2 Si 3 O 12 , Ca 3 Gd 2 Si 3 O 12 , Ca 3 Dy 2 Si 3 O 12 , Ca 3 Er 2 Si 3 O 12 and Ca 3 Lu 2 Si 3 O 12 ) have been determined using powder X-ray diffraction. From Rietveld refinement calculations on the collected powder patterns we observe a different distribution of the rare earth ions on the three available crystal sites characterized by different coordination numbers, depending on the ionic radius of the rare earth ion. The reasons of the instability of the silico-carnotite structure for lanthanide ions larger than Eu 3+ have been deduced. In addition, in order to detect crystal phase transitions, the powder patterns of Ca 3 Eu 2 Si 3 O 12 and Ca 3 Sm 2 Si 3 O 12 samples have been collected as a function of the temperature (RT-1000 °C range), but no phase transitions have been observed. - Graphical abstract: Synchrotron X-ray diffraction allows us the accurate determination of the RE 3+ ions distribution on the three available crystal sites of the silico-carnotite structure. Highlights: ► The structure of the Ca 3 M 2 Si 3 O 12 (M=Eu, Gd, Dy, Er and Lu) was determined. ► Different distribution of RE 3+ ions on the three available crystal sites was observed. ► The instability of the silico-carnotite structure for RE=La→Sm was discussed.

  19. Crystal Structure of a Trapped Catalytic Intermediate Suggests that Forced Atomic Proximity Drives the Catalysis of mIPS

    OpenAIRE

    Neelon, Kelly; Roberts, Mary F.; Stec, Boguslaw

    2011-01-01

    1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutant...

  20. TaRh2B2 and NbRh2B2: Superconductors with a chiral noncentrosymmetric crystal structure.

    Science.gov (United States)

    Carnicom, Elizabeth M; Xie, Weiwei; Klimczuk, Tomasz; Lin, Jingjing; Górnicka, Karolina; Sobczak, Zuzanna; Ong, Nai Phuan; Cava, Robert J

    2018-05-01

    It is a fundamental truth in solid compounds that the physical properties follow the symmetry of the crystal structure. Nowhere is the effect of symmetry more pronounced than in the electronic and magnetic properties of materials-even the projection of the bulk crystal symmetry onto different crystal faces is known to have a substantial impact on the surface electronic states. The effect of bulk crystal symmetry on the properties of superconductors is widely appreciated, although its study presents substantial challenges. The effect of a lack of a center of symmetry in a crystal structure, for example, has long been understood to necessitate that the wave function of the collective electron state that gives rise to superconductivity has to be more complex than usual. However, few nonhypothetical materials, if any, have actually been proven to display exotic superconducting properties as a result. We introduce two new superconductors that in addition to having noncentrosymmetric crystal structures also have chiral crystal structures. Because the wave function of electrons in solids is particularly sensitive to the host material's symmetry, crystal structure chirality is expected to have a substantial effect on their superconducting wave functions. Our two experimentally obtained chiral noncentrosymmetric superconducting materials have transition temperatures to superconductivity that are easily experimentally accessible, and our basic property characterization suggests that their superconducting properties may be unusual. We propose that their study may allow for a more in-depth understanding of how chirality influences the properties of superconductors and devices that incorporate them.

  1. Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose.

    Science.gov (United States)

    Brzezinski, Krzysztof; Dauter, Zbigniew; Jaskolski, Mariusz

    2012-02-01

    Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-β-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Å resolution. The fucose residue is exposed to solvent and is disordered. The enzyme-product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-L-glucosamine (penta-NAG). The structure has been determined at 1.98 Å resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop located between strand βC2 and helix αC3. In addition, there is a shift of the αC3 helix itself upon GDP

  2. Symmetry Groups of the Austenite Lattice and Construction of Self-Accommodation Complexes of Martensite Crystals in Alloys with the Shape-Memory Effect

    Science.gov (United States)

    Khundjua, A. G.; Ptitsin, A. G.; Brovkina, E. A.

    2018-01-01

    The internal structure of experimentally observed self-accommodation complexes of martensite crystals, which is determined by the system of twinning planes, is studied in this work. The direct correlation of the construction type of the complexes with the subgroups of the austenite lattice symmetry group is shown.

  3. Annealing effect of H+ -implanted single crystal silicon on strain and crystal structure

    International Nuclear Information System (INIS)

    Duo Xinzhong; Liu Weili; Zhang Miao; Gao Jianxia; Fu Xiaorong; Lin Chenglu

    2000-01-01

    The work focuses on the rocking curves of H + -implanted single silicon crystal detected by Four-Crystal X-ray diffractometer. The samples were annealed under different temperatures. Lattice defect in H + -implanted silicon crystals was detected by Rutherford Backscattering Spectrometry. It appeared that H-related complex did not crush until annealing temperature reached about 400 degree C. At that temperature H 2 was formed, deflated in silicon lattice and strained the lattice. But defects did not come into being in large quantity. The lattice was undamaged. When annealing temperature reached 500 degree C, strain induced by H 2 deflation crashed the silicon lattice. A large number of defects were formed. At the same time bubbles in the crystal and blister/flaking on the surface could be observed

  4. Crystal structure of aspartame anhydrate from powder diffraction data. Structural aspects of the dehydration process of aspartame

    NARCIS (Netherlands)

    Guguta, C.; Meekes, H.L.M.; Gelder, R. de

    2006-01-01

    Aspartame has three pseudo-polymorphic forms, two hydrates and a hemi-hydrate, for which crystal structures were determined from single-crystal diffraction data. This paper presents the crystal structure of the anhydrate, which was obtained by dehydrating the hemi-hydrate. The crystal structure of

  5. Crystal and molecular structure of dysprosium (3) n-aminobenzoate

    International Nuclear Information System (INIS)

    Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

    1981-01-01

    The X ray diffraction investigation of the Dy(NH 2 C 6 H 4 COO) 3 x3H 2 O complex is carried out. Triclinic crystals have lattice parameters α=11.095(15), b=9.099(17), c=12.780 (15)A, α=108.051(12), β=89.072(10); γ=104.954(12) 0 , space group P anti 1, Z=2. The structure consists of dimer molecules. The third water molecule in the formula is an outer spherical one. The average lengths of Dy-O and Dy-OH 2 are 2.39 and 2.40 A respectively, the average value of Dy-O in bridge carboxylates (2.26A) is remarkably shorter. Hydrogen bonds between amine ligand ends, carboxylic groups oxygen and water molecules bind complex molecules into the three-dimensional frame [ru

  6. Synthesis and Crystal Structure of Dinuclear Cadmium(II) Complex with Dipodal Ligand

    International Nuclear Information System (INIS)

    Kang, Young Jin; Moon, Suk Hee; Byun, Jong Chul; Park, Ki Min

    2010-01-01

    the preparation and structural characterization of the discrete dinuclear cadmium(II) complex with the formula [Cd(μ 2 -Cl) 2 Cl 2 ]· 2 (H 2 O)·0.5(CH 3 OH)·0.5(CH 3 CN) obtained from the reaction of CdCl 2 ·2.5H 2 O and podal ligand with quinoline end-groups has been reported. In two cadmium ions are triply bridged by two chloride and one donor atoms of ligand L and adopt distorted pentagonal bipyramidal geometries with seven coordinations. It is notable that example of discrete dinuclear complex which one podal ligand accommodates simultaneously two metal ions is very rare. During the last four decades, the chemistry of macrocyclic and non-cyclic polyethers has attracted an increasing attention because of their selective complexation, cation transport and enzyme chemistry. In the field of coordination chemistry, generally, non-cyclic, crown-type polyether affords the low complexation ability because of its conformational freedom while macrocyclic polyethers such as 18-crown-6 show the excellent complexing ability

  7. Crystal Structure of a Lipid G Protein-Coupled Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Michael A; Roth, Christopher B; Jo, Euijung; Griffith, Mark T; Scott, Fiona L; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M; Schuerer, Stephan C; Sanna, M Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C [Scripps; (Receptos)

    2012-03-01

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P1-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P1, resulting in the modulation of immune and stromal cell responses.

  8. Crystal structure of actinide metals at high compression

    International Nuclear Information System (INIS)

    Fast, L.; Soederlind, P.

    1995-08-01

    The crystal structures of some light actinide metals are studied theoretically as a function of applied pressure. The first principles electronic structure theory is formulated in the framework of density functional theory, with the gradient corrected local density approximation of the exchange-correlation functional. The light actinide metals are shown to be well described as itinerant (metallic) f-electron metals and generally, they display a crystal structure which have, in agreement with previous theoretical suggestions, increasing degree of symmetry and closed-packing upon compression. The theoretical calculations agree well with available experimental data. At very high compression, the theory predicts closed-packed structures such as the fcc or the hcp structures or the nearly closed-packed bcc structure for the light actinide metals. A simple canonical band picture is presented to explain in which particular closed-packed form these metals will crystallize at ultra-high pressure

  9. Crystal structure of Lymnaea stagnalis AChBP complexed with the potent nAChR antagonist DHβE suggests a unique mode of antagonism.

    Directory of Open Access Journals (Sweden)

    Azadeh Shahsavar

    Full Text Available Nicotinic acetylcholine receptors (nAChRs are pentameric ligand-gated ion channels that belong to the Cys-loop receptor superfamily. These receptors are allosteric proteins that exist in different conformational states, including resting (closed, activated (open, and desensitized (closed states. The acetylcholine binding protein (AChBP is a structural homologue of the extracellular ligand-binding domain of nAChRs. In previous studies, the degree of the C-loop radial extension of AChBP has been assigned to different conformational states of nAChRs. It has been suggested that a closed C-loop is preferred for the active conformation of nAChRs in complex with agonists whereas an open C-loop reflects an antagonist-bound (closed state. In this work, we have determined the crystal structure of AChBP from the water snail Lymnaea stagnalis (Ls in complex with dihydro-β-erythroidine (DHβE, which is a potent competitive antagonist of nAChRs. The structure reveals that binding of DHβE to AChBP imposes closure of the C-loop as agonists, but also a shift perpendicular to previously observed C-loop movements. These observations suggest that DHβE may antagonize the receptor via a different mechanism compared to prototypical antagonists and toxins.

  10. Complexes in the Ni2+-imidazole-RN(CH2COO-)2 systems. The crystal structures of tris(imidazole)iminodiacetatonickel(II) monohydrate, hexa(imidazole)nickel(II) bis(N-methyliminodiacetato)nickelate(II) hexahydrate, and tetra(aqua)bis(imidazole)nickel(II) bis(N-benzyliminodiacetato)nickelate(II)

    International Nuclear Information System (INIS)

    Polyakova, I.N.; Sergienko, V.S.; Poznyak, A.L.

    2000-01-01

    Crystals of different compositions, namely, [Ni(Ida)(Im) 3 ] · H 2 O (I), [Ni(Im) 6 ][Ni(Mida) 2 ] · 6H 2 O (II), and [Ni(Im) 2 (H 2 O) 4 ][Ni(Bida) 2 ] (III), have been precipitated from aqueous solutions of the Ni 2+ -Lig 2- Im systems, where Lig 2- is Ida, Mida, and Bida, respectively. The crystal structures of I-III are determined by X-ray diffraction analysis (R = 0.0307, 0.0348, and 0.0302 for 3061, 4706, and 2882 reflections, respectively). Crystals I are built of monomeric mixed-ligand complexes and molecules of crystallization water, which are interlinked by hydrogen bonds into a three-dimensional framework. In II and III, the ligands Lig 2- and Im form charged complexes separately. In II, the cationic and anionic layers of the complexes alternate along the c-axis. Numerous hydrogen bonds involving molecules of crystallization water link the layers into a three-dimensional framework. In III, the cationic and anionic complexes, which serve as proton donors and acceptors, respectively, are bound into layers parallel to the xy plane

  11. The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.

    Science.gov (United States)

    Jauch, Ralf; Ng, Calista K L; Narasimhan, Kamesh; Kolatkar, Prasanna R

    2012-04-01

    It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

  12. Solution structure of the Grb2 SH2 domain complexed with a high-affinity inhibitor

    International Nuclear Information System (INIS)

    Ogura, Kenji; Shiga, Takanori; Yokochi, Masashi; Yuzawa, Satoru; Burke, Terrence R.; Inagaki, Fuyuhiko

    2008-01-01

    The solution structure of the growth factor receptor-bound protein 2 (Grb2) SH2 domain complexed with a high-affinity inhibitor containing a non-phosphorus phosphate mimetic within a macrocyclic platform was determined by nuclear magnetic resonance (NMR) spectroscopy. Unambiguous assignments of the bound inhibitor and intermolecular NOEs between the Grb2 SH2 domain and the inhibitor was accomplished using perdeuterated Grb2 SH2 protein. The well-defined solution structure of the complex was obtained and compared to those by X-ray crystallography. Since the crystal structure of the Grb2 SH2 domain formed a domain-swapped dimer and several inhibitors were bound to a hinge region, there were appreciable differences between the solution and crystal structures. Based on the binding interactions between the inhibitor and the Grb2 SH2 domain in solution, we proposed a design of second-generation inhibitors that could be expected to have higher affinity

  13. Structural study of hydrogen and hydration by the IBARAKI biological crystal diffractometer (iBIX)/industrial use

    International Nuclear Information System (INIS)

    Tanaka, Ichiro; Hosoya, Takaaki; Kusaka, Katsuhiro; Niimura, Nobuo; Yamada, Taro; Tomoyori, Katsuaki; Yokoyama, Takeshi; Ohhara, Takashi; Kurihara, Kazuo; Ohnishi, Yuki; Yoshimura, Masashi; Kawamura, Takahiro; Oosumi, Takashi; Uchida, Hirohisa; Suzuki, Eiichiro; Kashiwagi, Tatsuki; Miyamoto, Akio; Furukawa, Yasunori

    2011-01-01

    IBARAKI Biological Crystal Diffractometer (iBIX), a new neutron diffractometer for protein crystallography, was constructed as a next generation neutron source in J-PARC (Japan Proton Accelerator Research Complex) and it has begun operation since December 2008. During a fiscal year of 2009, 14 detector units, the basic part of data reduction software and an equipment of cryostream cooler to 20K became available, and measurements and structural analysis of an organic standard crystal were succeeded. Since 120kW accelerator operation in December 2009, neutron measurements for structural analysis of several crystals of inorganic, organic compounds and proteins including industrial users' have been carried out and some of these data sets have been analyzed to the degree that positions of the hydrogen and the hydrated water could be identified. (author)

  14. Crystal structure and physical properties of a ruthenium(II) bipyridine dimethylsulfoxide complex

    International Nuclear Information System (INIS)

    Wang, Y.; Eichhorn, D.M.; Goswami, N.; Zhao, Q.; Rillema, D.P.

    1999-01-01

    The complex [Ru(bpy) 2 (DMSO)C1]PF 6 , where bpy is 2,2prime-bipyridine and DMSO is dimethyl-sulfoxide, crystallizes in the triclinic space group Pbar 1 (number s ign2) with a = 8.873 (2), b = 12.805 (4), c = 12.864 (4) angstrom, α = 97.76(3), β = 106.45(2), γ = 107.88(2); Z = 2, and d calc = 1.75 mg/m 3 . The coordination geometry is that of a distorted octahedron with a cis-RuN 4 SCl arrangement of coordinating atoms. The four Ru-N distances to the bpy ligands are 2.082(5), 2.092(4), 2.044(4), and 2.078(5) angstrom. The Ru-Cl distance is 2.421(2) angstrom and the Ru-S distance to DMSO is 2.260(1) angstrom. The Ru-N bond distance trans to Cl is the shortest; the Ru-N bond distance trans to S is the longest. The complex is oxidized and reduced reversibly at 1.13 and minus1.37 V vs. SSCE, respectively. It displays electronic absorptions at 515, 480 (1.5 x 10 4 ), 342 (1.5 X 10 4 ), 292 (1.2 X 10 5 ), and 240 nm (6.2 x 10 4 ) and has a broad emission band centered at 607 nm at 77 K in a 4:1 ethanol/methanol glass. The emission lifetime at room temperature is less than the pulse width of the laser, τ < 20 ns

  15. A monomeric copper-phosphoramide complex: synthesis, structure, and electronic properties

    Czech Academy of Sciences Publication Activity Database

    Henriques, Margarida Isabel Sousa; Gorbunov, D.I.; Ponomaryov, A.Y.; Saneei, A.; Pourayoubi, M.; Dušek, Michal; Zvyagin, S.; Uhlarz, M.; Wosnitza, J.

    2016-01-01

    Roč. 118, Nov (2016), s. 154-158 ISSN 0277-5387 R&D Projects: GA ČR(CZ) GA14-03276S; GA MŠk LO1603 EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : phosphoramide * magnetization * EPR * mononuclear copper complex * crystal structure Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.926, year: 2016

  16. Full analysis of feldspar texture and crystal structure by combining X-ray and electron techniques

    DEFF Research Database (Denmark)

    Balic Zunic, Tonci; Piazolo, Sandra; Katerinopoulou, Anna

    2013-01-01

    identification plus crystal structure refinement of all components in a feldspar intergrowth. This procedure was applied to perthitic intergrowths in feldspars from two different pegmatites in the Larvik plutonic complex in the southern part of the Oslo region, Norway. It revealed that the two starting high...

  17. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr; Shkurenko, Aleksander; Osior, Agnieszka; Kamieński, Bohdan; Szymański, Sławomir

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  18. Crystal structure of the bacterial luciferase/flavin complex provides insight into the function of the beta subunit.

    Science.gov (United States)

    Campbell, Zachary T; Weichsel, Andrzej; Montfort, William R; Baldwin, Thomas O

    2009-07-07

    Bacterial luciferase from Vibrio harveyi is a heterodimer composed of a catalytic alpha subunit and a homologous but noncatalytic beta subunit. Despite decades of enzymological investigation, structural evidence defining the active center has been elusive. We report here the crystal structure of V. harveyi luciferase bound to flavin mononucleotide (FMN) at 2.3 A. The isoalloxazine ring is coordinated by an unusual cis-Ala-Ala peptide bond. The reactive sulfhydryl group of Cys106 projects toward position C-4a, the site of flavin oxygenation. This structure also provides the first data specifying the conformations of a mobile loop that is crystallographically disordered in both prior crystal structures [(1995) Biochemistry 34, 6581-6586; (1996) J. Biol. Chem. 271, 21956 21968]. This loop appears to be a boundary between solvent and the active center. Within this portion of the protein, a single contact was observed between Phe272 of the alpha subunit, not seen in the previous structures, and Tyr151 of the beta subunit. Substitutions at position 151 on the beta subunit caused reductions in activity and total quantum yield. Several of these mutants were found to have decreased affinity for reduced flavin mononucleotide (FMNH(2)). These findings partially address the long-standing question of how the beta subunit stabilizes the active conformation of the alpha subunit, thereby participating in the catalytic mechanism.

  19. Structural Color Patterns by Electrohydrodynamic Jet Printed Photonic Crystals.

    Science.gov (United States)

    Ding, Haibo; Zhu, Cun; Tian, Lei; Liu, Cihui; Fu, Guangbin; Shang, Luoran; Gu, Zhongze

    2017-04-05

    In this work, we demonstrate the fabrication of photonic crystal patterns with controllable morphologies and structural colors utilizing electrohydrodynamic jet (E-jet) printing with colloidal crystal inks. The final shape of photonic crystal units is controlled by the applied voltage signal and wettability of the substrate. Optical properties of the structural color patterns are tuned by the self-assembly of the silica nanoparticle building blocks. Using this direct printing technique, it is feasible to print customized functional patterns composed of photonic crystal dots or photonic crystal lines according to relevant printing mode and predesigned tracks. This is the first report for E-jet printing with colloidal crystal inks. Our results exhibit promising applications in displays, biosensors, and other functional devices.

  20. Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate.

    Science.gov (United States)

    Chen, Yaozong; Jiang, Yiping; Guo, Zhihong

    2016-12-06

    o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.

  1. Crystal structures of palladium(II) ternary complexes of 5-x-2-aminobenzoic acid with 1,10-phenanthroline and their interaction with calf thymus DNA (where X=Cl, Br and I).

    Science.gov (United States)

    Wang, Yue; Okabe, Nobuo; Odoko, Mamiko

    2005-10-01

    The crystal structures of a series of three palladium(II) ternary complexes of 5-halogeno-2-aminobenzoic acid (5-X-AB, where X=Cl, Br and I) with 1,10-phenanthroline [Pd(5-Cl-AB)(phen)] (1), [Pd(5-Br-AB)(phen)] (2) and [Pd(5-I-AB)(phen)] (3) have been determined, and their coordination geometries and the crystal architecture characterized. All of the complexes are an isostructure in which each Pd(II) atom has basically similar square planar coordination geometry. The substitute halogen group at 5-position of AB plays an important role in producing the coordination bonds of the carboxylate and amino groups in which the carboxylate O atom and the amino N atom act as the negative monodentate ligand atoms. The coordination bond distances of O-Pd increase in the order 1<2<3, while those of N-Pd decrease in the same order. The binding of the complexes to the calf thymus DNA has also been studied by the fluorescence method. Each of the complexes shows high binding propensity to DNA which can be reflected as the relative order 1<2<3.

  2. SYNTHESIS, CHARACTERIZATION, AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

    a

    KEY WORDS: Barium, Crystal structure, 2,6-Pyridinedicarboxylic acid .... The rational design of novel metal-organic frameworks has attracted great ..... Bond, A.D.; Jones, W. Supramolecular Organization and Materials Design, Jones, W.; Rao,.

  3. Preparation and properties of crystals of mixed refractory oxides with perovskite structure

    Energy Technology Data Exchange (ETDEWEB)

    Melekh, B T; Andreev, A A; Kartenko, N F; Pevtsov, A B; Trepakov, V A; Filin, Yu N [AN SSSR, Moscow. Fiziko-Tekhnicheskij Inst.

    1982-10-01

    Peculiar features of crystal growth of some complex refractory oxides with perovskite structure using the method of direct high-frequency melting in a cold container are studied. Melting, synthesis and directed crystallization have been conducted in the air. X-ray diffraction investigations of the prepared SrTiO/sub 3/, CaZrO/sub 3/, BaZrO/sub 3/, BaHFO/sub 3/, LaCrO/sub 3/, YCrO/sub 3/, ErCrO/sub 3/, La/sub 2/Ti/sub 2/O/sub 7/, LaTaO/sub 3/ and other oxides are conducted, lattice parameters are given. Optical spectra of absorption, photo- and thermoluminescence and thermostimulated currents are studied.

  4. Crystal structures of β-galactosidase from Penicillium sp. and its complex with galactose

    International Nuclear Information System (INIS)

    Rojas, A.L.; Nagem, R.A.P.; Garratt, R.C.; Polikarpov, I.; Neustroev, K.N.; Eneyskaya, E.V.; Kulminskaya, A.A.; Golubev, A.M.; Arand, M.; Adamska, M.

    2004-01-01

    Glycosidase belong to a group of enzymes displaying a great variety of protein folds and substrate specificities. Two critically located acidic residues make up the catalytic machinery of these enzymes, which are responsible for the cleavage of glycosidic bonds. The applications of glycosidase in textile, food, and pulp processing and in catalysts and oligosaccharide synthesis have encouraged the engineering of these proteins to improve their catalytic properties and stability. Furthermore, structural studies broaden our understanding of the catalytic mechanism and the role of glycosidase in the recognition processes of their different substrates. In this work, we describe crystallographic studies of a fungi glycosidase. The crystallographic structures of β-galactosidase from Penicillium sp. and its complex with galactose were solved at 1.90 A and 2.10 A resolution, respectively. The X-ray structure of the enzyme-galactose complex was useful in identifying the residue Glu200 as the proton donor and residue Glu 299 as the nucleophiles involved in catalysis. (author)

  5. Crystal structures of {beta}-galactosidase from Penicillium sp. and its complex with galactose

    Energy Technology Data Exchange (ETDEWEB)

    Rojas, A.L.; Nagem, R.A.P.; Garratt, R.C.; Polikarpov, I. [Universidade de Sao Paulo, Sao Carlos, SP (Brazil); Neustroev, K.N.; Eneyskaya, E.V.; Kulminskaya, A.A.; Golubev, A.M. [St. Petersburg, Gatchina (Russian Federation); Arand, M.; Adamska, M. [University of Wuerzburg (Germany)

    2004-07-01

    Glycosidase belong to a group of enzymes displaying a great variety of protein folds and substrate specificities. Two critically located acidic residues make up the catalytic machinery of these enzymes, which are responsible for the cleavage of glycosidic bonds. The applications of glycosidase in textile, food, and pulp processing and in catalysts and oligosaccharide synthesis have encouraged the engineering of these proteins to improve their catalytic properties and stability. Furthermore, structural studies broaden our understanding of the catalytic mechanism and the role of glycosidase in the recognition processes of their different substrates. In this work, we describe crystallographic studies of a fungi glycosidase. The crystallographic structures of {beta}-galactosidase from Penicillium sp. and its complex with galactose were solved at 1.90 A and 2.10 A resolution, respectively. The X-ray structure of the enzyme-galactose complex was useful in identifying the residue Glu200 as the proton donor and residue Glu 299 as the nucleophiles involved in catalysis. (author)

  6. Synthesis, crystal structure and excellent photoluminescence properties of copper (II and cobalt (II complexes with Bis(1[(4-butylphenylimino]methyl naphthalen-2-ol Schiff base

    Directory of Open Access Journals (Sweden)

    V.B. Nagaveni

    2018-03-01

    Full Text Available Copper (II and Cobalt (II metal complexes (4a- and 4b-complexes using Schiff base ligand 1-[(4-butylphenylimino]methyl naphthalen-2-ol (3 have been synthesized. The single crystals of Copper (II and Cobalt (II complex phosphors were grown and characterized by Fourier-Transform Infrared (FT-IR, single crystal X-ray diffraction (XRD, SEM (Scanning Electron Microscope and EDS (Energy Dispersive X-ray spectroscopy. Photoluminescence study of the phosphors revealed the presence of excitation peaks at 333 nm and 360 nm for 4a-complex (λemi = 495 nm and excitation peaks at 300 nm and 360 nm for 4b-complex (λemi = 496 nm. The calculated CCT values of the complexes pointed out that these materials can be used to obtain cold white light from the light emitting devices. Diffuse reflectance spectra (DRS showed the measured band gap energies of 1.78 eV and 1.44 eV for Cu (II and Co (II complexes, respectively. It is concluded that the 4a- and 4b-complexes become white and blue green light emitting diodes respectively and will be useful in the development of strong electroluminescent materials. Keywords: 1[(4-butylphenylimino]methylnaphthalen-2-ol, Schiff base, Cu (II and Co (IIcomplex, Photoluminescence, Single crystal XRD, OLED

  7. Ruthenium(II) bipyridine complexes bearing quinoline-azoimine (NN'N″) tridentate ligands: synthesis, spectral characterization, electrochemical properties and single-crystal X-ray structure analysis.

    Science.gov (United States)

    Al-Noaimi, Mousa; Abdel-Rahman, Obadah S; Fasfous, Ismail I; El-khateeb, Mohammad; Awwadi, Firas F; Warad, Ismail

    2014-05-05

    Four octahedral ruthenium(II) azoimine-quinoline complexes having the general molecular formula [Ru(II)(L-Y)(bpy)Cl](PF6) {L-Y=YC6H4N=NC(COCH3)=NC9H6N, Y=H (1), CH3 (2), Br (3), NO2 (4) and bpy=2,2'-bipyrdine} were synthesized. The azoimine-quinoline based ligands behave as NN'N″ tridentate donors and coordinated to ruthenium via azo-N', imine-N' and quinolone-N″ nitrogen atoms. The composition of the complexes has been established by elemental analysis, spectral methods (FT-IR, electronic, (1)H NMR, UV/Vis and electrochemical (cyclic voltammetry) techniques. The crystal structure of complex 1 is reported. The Ru(II) oxidation state is greatly stabilized by the novel tridentate ligands, showing Ru(III/II) couples ranging from 0.93-1.27 V vs. Cp2Fe/Cp2Fe(+). The absorption spectrum of 1 in dichloromethane was modeled by time-dependent density functional theory (TD-DFT). Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine.

    Science.gov (United States)

    Narayana, N; Cox, S; Shaltiel, S; Taylor, S S; Xuong, N

    1997-04-15

    The crystal structure of the hexahistidine-tagged mouse recombinant catalytic subunit (H6-rC) of cAMP-dependent protein kinase (cAPK), complexed with a 20-residue peptide inhibitor from the heat-stable protein kinase inhibitor PKI(5-24) and adenosine, was determined at 2.2 A resolution. Novel crystallization conditions were required to grow the ternary complex crystals. The structure was refined to a final crystallographic R-factor of 18.2% with good stereochemical parameters. The "active" enzyme adopts a "closed" conformation as found in rC:PKI(5-24) [Knighton et al. (1991a,b) Science 253, 407-414, 414-420] and packs in a similar manner with the peptide providing a major contact surface. This structure clearly defines the subsites of the unique nucleotide binding site found in the protein kinase family. The adenosine occupies a mostly hydrophobic pocket at the base of the cleft between the two lobes and is completely buried. The missing triphosphate moiety of ATP is filled with a water molecule (Wtr 415) which replaces the gamma-phosphate of ATP. The glycine-rich loop between beta1 and beta2 helps to anchor the phosphates while the ribose ring is buried beneath beta-strand 2. Another ordered water molecule (Wtr 375) is pentacoordinated with polar atoms from adenosine, Leu 49 in beta-strand 1, Glu 127 in the linker strand between the two lobes, Tyr 330, and a third water molecule, Wtr 359. The conserved nucleotide fold can be defined as a lid comprised of beta-strand 1, the glycine-rich loop, and beta-strand 2. The adenine ring is buried beneath beta-strand 1 and the linker strand (120-127) that joins the small and large lobes. The C-terminal tail containing Tyr 330, a segment that lies outside the conserved core, covers this fold and anchors it in a closed conformation. The main-chain atoms of the flexible glycine-rich loop (residues 50-55) in the ATP binding domain have a mean B-factor of 41.4 A2. This loop is quite mobile, in striking contrast to the other

  9. Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments

    International Nuclear Information System (INIS)

    Hörer, Stefan; Reinert, Dirk; Ostmann, Katja; Hoevels, Yvette; Nar, Herbert

    2013-01-01

    A mutant of the Kelch domain of the human Keap1 protein has been designed in order to enable the soaking of small-molecule ligands. The apo structure of this mutant is reported at 1.98 Å resolution and the suitability of the crystal system has been demonstrated by the structure of the mutated Keap1 Kelch domain in complex with a cyclic peptide derived from Nrf2. Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of Nrf2. Oxidative stress prevents the degradation of Nrf2 and leads to the activation of cytoprotective genes. Therefore, Keap1 is an attractive drug target in inflammatory diseases. The support of a medicinal chemistry effort by structural research requires a robust crystallization system in which the crystals are preferably suited for performing soaking experiments. This facilitates the generation of protein–ligand complexes in a routine and high-throughput manner. The structure of human Keap1 has been described previously. In this crystal form, however, the binding site for Nrf2 was blocked by a crystal contact. This interaction was analysed and mutations were introduced to disrupt this crystal contact. One double mutation (E540A/E542A) crystallized in a new crystal form in which the binding site for Nrf2 was not blocked and was accessible to small-molecule ligands. The crystal structures of the apo form of the mutated Keap1 Kelch domain (1.98 Å resolution) and of the complex with an Nrf2-derived peptide obtained by soaking (2.20 Å resolution) are reported

  10. Molybdenum peroxo complex. Structure and thermal behavior

    Energy Technology Data Exchange (ETDEWEB)

    Segawa, Koichi; Ooga, Katsumi; Kurusu, Yasuhiko

    1984-10-01

    The molybdenum peroxide (Mo-y) prepared by oxidation of molybdenum metal with hydrogen peroxide has been studied to determine its structure and thermal behavior. Temperature programmed decomposition has been used to study the thermal stability of Mo-y. Two distinct peaks, I and II, of decomposition processes are discernible in Mo-y. Peak I corresponds to the elimination of water of crystallization and peak II to the decomposition of a peroxide ion of Mo-y. IR and UV examinations support the results of the thermal analysis. The IR band at 931 cm/sup -1/ and the UV band at 381 nm show the same thermal behavior. Both bands are attributable to the peroxide ion of Mo-y. Spectroscopic studies show that Mo-y has the tetrahedral coordination derived from the single molybdenum complex, which has double bond oxygens attached to Mo atom and has a symmetric type of peroxide ion with one water of crystallization.

  11. Mutation and crystallization of the first KH domain of human polycytosine-binding protein 1 (PCBP1) in complex with DNA

    International Nuclear Information System (INIS)

    Yoga, Yano M. K.; Traore, Daouda A. K.; Wilce, Jacqueline A.; Wilce, Matthew C. J.

    2011-01-01

    The successful preparation of a mutant KH domain representing the first KH domain of PCBP1 and its crystallization in complex with a C-rich DNA are reported. This structure is anticipated to provide high-resolution information that will allow better understanding of the basis of cytosine specificity by PCBPs. Polycytosine-binding proteins (PCBPs) are triple KH-domain proteins that play an important role in the regulation of translation of eukaryotic mRNA. They are also utilized by viral RNA and have been shown to interact with ssDNA. Underlying their function is the specific recognition of C-rich nucleotides by their KH domains. However, the structural basis of this recognition is only partially understood. Here, the preparation of a His-tagged KH domain is described, representing the first domain of PCBP1 that incorporates a C54S mutation as well as the addition of a C-terminal tryptophan. This construct has facilitated the preparation of highly diffracting crystals in complex with C-rich DNA (sequence ACCCCA). Crystals of the KH1–DNA complex were grown using the hanging-drop vapour-diffusion method in 0.1 M phosphate–citrate pH 4.2, 40%(v/v) PEG 300. X-ray diffraction data were collected to 1.77 Å resolution and the diffraction was consistent with space group P2 1 , with unit-cell parameters a = 38.59, b = 111.88, c = 43.42 Å, α = γ = 90.0, β = 93.37°. The structure of the KH1–DNA complex will further our insight into the basis of cytosine specificity by PCBPs

  12. Crystallization and crystallographic analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA mutant DhaA31 and its complex with 1,2,3-trichloropropane

    International Nuclear Information System (INIS)

    Lahoda, Maryna; Chaloupkova, Radka; Stsiapanava, Alena; Damborsky, Jiri; Kuta Smatanova, Ivana

    2011-01-01

    A mutant of the haloalkane dehalogenase DhaA (DhaA31) from R. rhodochrous NCIMB 13064 and its complex with 1,2,3-trichloropropane were crystallized and the crystals diffracted to high resolution. Haloalkane dehalogenases hydrolyze carbon–halogen bonds in a wide range of halogenated aliphatic compounds. The potential use of haloalkane dehalogenases in bioremediation applications has stimulated intensive investigation of these enzymes and their engineering. The mutant DhaA31 was constructed to degrade the anthropogenic compound 1,2,3-trichloropropane (TCP) using a new strategy. This strategy enhances activity towards TCP by decreasing the accessibility of the active site to water molecules, thereby promoting formation of the activated complex. The structure of DhaA31 will help in understanding the structure–function relationships involved in the improved dehalogenation of TCP. The mutant protein DhaA31 was crystallized by the sitting-drop vapour-diffusion technique and crystals of DhaA31 in complex with TCP were obtained using soaking experiments. Both crystals belonged to the triclinic space group P1. Diffraction data were collected to high resolution: to 1.31 Å for DhaA31 and to 1.26 Å for DhaA31 complexed with TCP

  13. Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Prem [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India); Talawar, Ramappa K.; Krishna, P. D. V.; Varshney, Umesh [Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012 (India); Vijayan, M., E-mail: mv@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India)

    2006-12-01

    Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis.

  14. Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

    International Nuclear Information System (INIS)

    Singh, Prem; Talawar, Ramappa K.; Krishna, P. D. V.; Varshney, Umesh; Vijayan, M.

    2006-01-01

    Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis

  15. Crystal structure of enolase from Drosophila melanogaster.

    Science.gov (United States)

    Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

    2017-04-01

    Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

  16. The structural basis of actin filament branching by the Arp2/3 complex

    OpenAIRE

    Rouiller, Isabelle; Xu, Xiao-Ping; Amann, Kurt J.; Egile, Coumaran; Nickell, Stephan; Nicastro, Daniela; Li, Rong; Pollard, Thomas D.; Volkmann, Niels; Hanein, Dorit

    2008-01-01

    The actin-related protein 2/3 (Arp2/3) complex mediates the formation of branched actin filaments at the leading edge of motile cells and in the comet tails moving certain intracellular pathogens. Crystal structures of the Arp2/3 complex are available, but the architecture of the junction formed by the Arp2/3 complex at the base of the branch was not known. In this study, we use electron tomography to reconstruct the branch junction with sufficient resolution to show how the Arp2/3 complex in...

  17. Crystallization and preliminary X-ray crystallographic studies of a Lys49-phospholipase A2 homologue from Bothrops pirajai venom complexed with rosmarinic acid

    International Nuclear Information System (INIS)

    Santos, Juliana I. dos; Santos-Filho, Norival A.; Soares, Andreimar M.; Fontes, Marcos R. M.

    2010-01-01

    PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A 2 from B. pirajai venom, was cocrystallized with the inhibitor rosmarinic acid from C. verbenacea. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved, indicating a remarkable electronic density for the ligand at the entrance to the hydrophobic channel. PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A 2 from Bothrops pirajai venom, was crystallized in the presence of the inhibitor rosmarinic acid (RA). This is the active compound in the methanolic extract of Cordia verbenacea, a plant that is largely used in Brazilian folk medicine. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved by molecular-replacement techniques, showing electron density that corresponds to RA molecules at the entrance to the hydrophobic channel. The crystals belong to space group P2 1 2 1 2 1 , indicating conformational changes in the structure after ligand binding: the crystals of all apo Lys49-phospholipase A 2 structures belong to space group P3 1 21, while the crystals of complexed structures belong to space groups P2 1 or P2 1 2 1 2 1

  18. Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

    Energy Technology Data Exchange (ETDEWEB)

    Wubben, T.; Mesecar, A.D. (Purdue); (UIC)

    2014-10-02

    Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observed in the MtPPAT-CoA complex.

  19. Luminescent lanthanide complexes with 4-acetamidobenzoate: Synthesis, supramolecular assembly via hydrogen bonds, crystal structures and photoluminescence

    International Nuclear Information System (INIS)

    Yin Xia; Fan Jun; Wang Zhihong; Zheng Shengrun; Tan Jingbo; Zhang Weiguang

    2011-01-01

    Four new luminescent complexes, namely, [Eu(aba) 2 (NO 3 )(C 2 H 5 OH) 2 ] (1), [Eu(aba) 3 (H 2 O) 2 ].0.5 (4, 4'-bpy).2H 2 O (2), [Eu 2 (aba) 4 (2, 2'-bpy) 2 (NO 3 ) 2 ].4H 2 O (3) and [Tb 2 (aba) 4 (phen) 2 (NO 3 ) 2 ].2C 2 H 5 OH (4) were obtained by treating Ln(NO 3 ) 3 .6H 2 O and 4-acetamidobenzoic acid (Haba) with different coligands (4, 4'-bpy=4, 4'-bipyridine, 2, 2'-bpy=2, 2'-bipyridine, and phen=1, 10-phenanthroline). They exhibit 1D chains (1-2) and dimeric structures (3-4), respectively. This structural variation is mainly attributed to the change of coligands and various coordination modes of aba molecules. Moreover, the coordination units are further connected via hydrogen bonds to form 2D even 3D supramolecular networks. These complexes show characteristic emissions in the visible region at room temperature. In addition, thermal behaviors of four complexes have been investigated under air atmosphere. The relationship between the structures and physical properties has been discussed. - Graphical abstract: Structure variation of four complexes is attributed to the change of coligands and various coordination modes of aba molecules. Moreover, they show characteristic emissions in the visible region. Highlights: → Auxiliary ligands have played the crucial roles on the structures of the resulting complexes. → Isolated structure units are further assembled via H-bonds to form supramolecular networks. → These solid-state complexes exhibit strong, characteristic emissions in the visible region.

  20. Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form

    Directory of Open Access Journals (Sweden)

    Boguslaw Stec

    2007-10-01

    Full Text Available We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCOfrom the red algae Galdieria Sulphuraria. The protein crystallized in two different crystalforms, the I422 crystal form being obtained from high salt and the P21 crystal form beingobtained from lower concentration of salt and PEG. We report here the crystallization,preliminary stages of structure determination and the detection of the structural phasetransition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzymebelongs to the hexadecameric class (L8S8 with an approximate molecular weight 0.6MDa.The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a singlehexadecamer per asymmetric unit. The preservation of diffraction power in a phasetransition for such a large macromolecule is rare.

  1. Complexes of uranyl nitrate with 2,6-pyridinedicarboxamides: synthesis, crystal structure, and DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Alyapyshev, Mikhail; Babain, Vasiliy [ITMO University, 49, Kronverksky pr., 197101, St. Petersburg (Russian Federation); ThreeArc Mining Ltd., 5, Stary Tolmachevskiy per., 115184, Moscow (Russian Federation); Tkachenko, Lyudmila; Lumpov, Alexander [Khlopin Radium Institute, 28, 2nd Murinskiy pr., 194021, St. Petersburg (Russian Federation); Gurzhiy, Vladislav; Zolotarev, Andrey; Dar' in, Dmitriy [St. Petersburg State University, 7-9, Universitetskaya nab., 199034, St. Petersburg (Russian Federation); Ustynyuk, Yuriy; Gloriozov, Igor [M.V. Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Paulenova, Alena [Department of Nuclear Engineering, Oregon State University, Corvallis, OR (United States)

    2017-05-04

    Two complexes of uranyl nitrate with N,N,N',N'-tetrabutyl-2,6-pyridinedicarboxamide (TBuDPA) and N,N'-diethyl-N,N'-diphenyl-2,6-pyridinedicarboxamide (EtPhDPA) were synthesized and studied. The complex of tetraalkyl-2,6-pyridinedicarboxamide with metal nitrate was synthesized for the first time. XRD analysis revealed the different type of complexation: a 1:1 metal:ligand complex for EtPhDPA and complex with polymeric structure for TBuDPA. The quantum chemical calculations (DFT) confirm that both ligands form the most stable complexes that match the minimal values pre-organization energy of the ligands. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  2. Rotational and translational distortions of the crystal structure of the Sr2HrRuO6 (Hr = Ho, Dy, Gd, Eu) complex perovskites

    International Nuclear Information System (INIS)

    Triana, C.A.; Landínez Téllez, D.A.; Roa-Rojas, J.

    2013-01-01

    Sr 2 HrRuO 6 (Hr = Ho, Dy, Gd, Eu) complex perovskites were synthesized through the high-temperature solid-state reaction method, and their crystal structures were analyzed in detail as a function of the Hr-cation ionic radius. Results of powder XRD pattern measurement and Rietveld analysis of the experimental profiles show that the Sr 2 HrRuO 6 compounds crystallize in a monoclinic distorted perovskite-like structure, P2 1 /n (#14) space group, where the unit cell parameters are related to the primitive unit cell a p by a≈√(2)a p , b≈√(2)a p and c ≈ 2a p . The structures show an alternate distribution of the Ru 5+ (2d: 0.5, 0, 0) and Hr 3+ (2c: 0, 0.5, 0) making up RuO 6 and HrO 6 octahedra alternatively arranged in two interleaving fcc sublattices, where the O(1), O(2), and O(3) ions are localized at the corner of the octahedral, while the Sr 2+ is located at the A-site, occupying the cavities built by the corner-sharing octahedra with Wyckoff position 4e. Due to the existence of mismatched ionic sizes between the ionic radii of the Sr 2 HrRuO 6 compounds, the HrO 6 and RuO 6 octahedra are constrained to tilting around the [111] c , [001] c , and [110] c cubic directions so as to optimize the Sr–O inter-atomic bond lengths, tending to rotate the structure in order to fix the Ru 5+ and Hr 3+ ions on the M′ and M″ sites of the complex perovskites. The cell parameters a, b, and c, the inter-atomic bond angles, the inter-atomic bond lengths, and the tilting angles increase as the Hr-cation ionic radius increases. The mismatch that exists in the Sr 2 HrRuO 6 ionic radius produces a large distortion from the ideal cubic symmetry. The pure perovskite-like phase of Sr 2 HrRuO 6 is thermodynamically and kinetically stable at high temperatures above 1420 K, where it is entirely governed by the average size of the Hr 3+ and Ru 5+ cations. Highlights: ► Crystal structure of Sr 2 HrRuO 6 (Hr = Ho, Dy, Gd, Eu) as a function of Hr ionic radius. ► XRD

  3. Crystal structures, DFT calculations, and Hirshfeld surface analyses of two new copper(II) and nickel(II) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

    Science.gov (United States)

    Seifikar Ghomi, Leila; Behzad, Mahdi; Tarahhomi, Atekeh; Arab, Ali

    2017-12-01

    Two new Ni(II) and Cu(II) complexes of a tetradentate Schiff base ligand (1 and 2, respectively), derived from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-6-methoxy benzaldehyde, were synthesized and characterized by IR, UV-Vis, 1H NMR spectroscopy, and X-Ray crystallography. The central metal ions in both complexes are coordinated via the N2O2 coordination sphere of the ligand with square-planar geometry. DFT results revealed that the Msbnd N and Msbnd O interactions (M = Ni, Cu) are weaker than the typical covalent single bond indicating that ionic and electrostatic interactions are dominated in Msbnd N and Msbnd O bonds. Hirshfeld surface (HS) analyses of the studied structures 1 and 2 have been performed. The study using 3D HSs and 2D fingerprint plots (FPs) highlighted the dominant contacts H⋯H, C⋯H/H⋯C and O⋯H/H⋯O in both structures, and H⋯Cl in 2. The molecular assemblies held by C⋯O/O⋯C (in 1) and C⋯C (in 1 and 2) type dipole-dipole interactions are also found in the crystal packing contributing towards stability. The significant contributions arising from the mentioned interactions in crystal packing are also revealed from the Hirshfeld surface FPs showing a major contribution to total HS area for the H⋯H contacts for both structures.

  4. Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N4-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer

    Science.gov (United States)

    Jayakumar, K.; Sithambaresan, M.; Aiswarya, N.; Kurup, M. R. Prathapachandra

    2015-03-01

    Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N4-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ = 0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)sbnd I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g|| > g⊥ > 2.0023 and the g values in frozen DMF are consistent with the dx2-y2 ground state. The thermal stabilities of some of the complexes were also determined.

  5. Formation of nano-hydroxyapatite crystal in situ in chitosan-pectin polyelectrolyte complex network

    International Nuclear Information System (INIS)

    Li Junjie; Zhu Dunwan; Yin Jianwei; Liu Yuxi; Yao Fanglian; Yao Kangde

    2010-01-01

    Hydroxyapatite (HA)/polysaccharide composites have been widely used in bone tissue engineering due to their chemical similarity to natural bone. Polymer matrix-mediated synthesis of nano-hydroxyapatite is one of the simplest models for biomimetic. In this article, the nano-hydroxyapatite/chitosan-pectin (nHCP) composites were prepared through in situ mineralization of hydroxyapatite in chitosan-pectin polyelectrolyte complex (PEC) network. The formation processes of nHCP were investigated by X-ray diffraction (XRD) analysis. The interactions between nHA crystal and chitosan-pectin PEC networks were studied using Fourier Transform Infrared Spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC). The morphology and structure of nHA crystal were characterized by XRD and Transmission Electron Microscope (TEM). Results suggested that the interfacial interactions between nano-hydroxyapatite crystal and chitosan-pectin PEC network assist the site specific nucleation and growth of nHA nanoparticles. The nHA crystals grow along the c-axis. In this process, pH value is the main factor to control the nucleation and growth of nHA crystal in chitosan-pectin PEC networks, because both the interactions' strength between nHA crystal and chitosan-pectin and diffusion rate of inorganic ions depend on the pH value of the reaction system. Apart from the pH value, the chitosan/pectin ratio and [Ca 2+ ] also take important effects on the formation of nHA crystal. An effective way to control the size of nHA crystal is to adjust the content of pectin and [Ca 2+ ]. It is interesting that the Zeta potential of nHCP composites is about - 30 mV when the chitosan/pectin ratio ≤ 1:1, and the dispersion solution of nHCP composites has higher stability, which provides the possibility to prepare 3D porous scaffolds with nHCP for bone tissue engineering.

  6. Formation of nano-hydroxyapatite crystal in situ in chitosan-pectin polyelectrolyte complex network

    Energy Technology Data Exchange (ETDEWEB)

    Li Junjie [Department of Polymer Science and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 (China); Research Institute of Polymeric Materials, Tianjin University, Tianjin, 300072 (China); Zhu Dunwan [Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300072 (China); Yin Jianwei; Liu Yuxi [Department of Polymer Science and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 (China); Yao Fanglian, E-mail: yaofanglian@tju.edu.cn [Department of Polymer Science and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 (China); Yao Kangde [Research Institute of Polymeric Materials, Tianjin University, Tianjin, 300072 (China)

    2010-07-20

    Hydroxyapatite (HA)/polysaccharide composites have been widely used in bone tissue engineering due to their chemical similarity to natural bone. Polymer matrix-mediated synthesis of nano-hydroxyapatite is one of the simplest models for biomimetic. In this article, the nano-hydroxyapatite/chitosan-pectin (nHCP) composites were prepared through in situ mineralization of hydroxyapatite in chitosan-pectin polyelectrolyte complex (PEC) network. The formation processes of nHCP were investigated by X-ray diffraction (XRD) analysis. The interactions between nHA crystal and chitosan-pectin PEC networks were studied using Fourier Transform Infrared Spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC). The morphology and structure of nHA crystal were characterized by XRD and Transmission Electron Microscope (TEM). Results suggested that the interfacial interactions between nano-hydroxyapatite crystal and chitosan-pectin PEC network assist the site specific nucleation and growth of nHA nanoparticles. The nHA crystals grow along the c-axis. In this process, pH value is the main factor to control the nucleation and growth of nHA crystal in chitosan-pectin PEC networks, because both the interactions' strength between nHA crystal and chitosan-pectin and diffusion rate of inorganic ions depend on the pH value of the reaction system. Apart from the pH value, the chitosan/pectin ratio and [Ca{sup 2+}] also take important effects on the formation of nHA crystal. An effective way to control the size of nHA crystal is to adjust the content of pectin and [Ca{sup 2+}]. It is interesting that the Zeta potential of nHCP composites is about - 30 mV when the chitosan/pectin ratio {<=} 1:1, and the dispersion solution of nHCP composites has higher stability, which provides the possibility to prepare 3D porous scaffolds with nHCP for bone tissue engineering.

  7. Unexpected ferromagnetic interaction in a new tetranuclear copper(II) complex: synthesis, crystal structure, magnetic properties, and theoretical studies.

    Science.gov (United States)

    Fondo, Matilde; García-Deibe, Ana M; Corbella, Monstserrat; Ruiz, Eliseo; Tercero, Javier; Sanmartín, Jesús; Bermejo, Manuel R

    2005-07-11

    The new tetranuclear carbonate complex [Cu2L)2(CO3)] x 8H2O (1 x 8H2O) (H3L = (2-(2-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) has been obtained by two different synthetic routes and fully characterized. Recrystallization of 1 x 8H2O in methanol yields single crystals of {[(Cu2L)2(CO3)]}2 x 12H2O (1 x 6H2O), suitable for X-ray diffraction studies. The crystal structure of 1 x 6H2O shows two crystallographically different tetranuclear molecules in the asymmetric unit, 1a and 1b. Both molecules can be understood as self-assembled from two dinuclear [Cu2L]+ cations, joined by a mu4-eta(2):eta(1):eta(1) carbonate ligand. The copper atoms of each crystallographically different [(Cu2L)2(CO3)] molecule present miscellaneous coordination polyhedra: in both 1a and 1b, two metal centers are in square pyramidal environments, one displays a square planar chromophore and the other one has a geometry that can be considered as an intermediate between square pyramid and trigonal bipyramid. Magnetic studies reveal net intramolecular ferromagnetic coupling between the metal atoms. Density functional calculations allow the assignment of the different magnetic coupling constants and explain the unexpected ferromagnetic behavior, because of the presence of an unusual NCN bridging moiety and countercomplementarity of the phenoxo (or carbonate) and NCN bridges.

  8. Synthesis, characterization and single crystal x-ray analysis of a complex of iron(II) bis(2,4-dimethylphenyl)dithiophosphate with 4-ethylpyridine

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Sandeep; Andotra, Savit; Kaur, Mandeep [University of Jammu, Department of Chemistry (India); Gupta, Vivek K.; Kant, Rajni [Department of Physics and Electronics, University of Jammu, X-ray Crystallographic Laboratory (India); Pandey, Sushil K., E-mail: kpsushil@rediffmail.com [University of Jammu, Department of Chemistry (India)

    2016-09-15

    Complex of iron(II) bis(2,4-dimethylphenyl)dithiophosphate with 4-ethylpyridine [((2,4- (CH{sub 3}){sub 2}C{sub 6}H{sub 3}O)2PS2)2Fe(NC{sub 5}H{sub 4}(C{sub 2}H{sub 5})-4){sub 2}] is synthesized and characterized by elemental analysis, magnetic moment, IR spectroscopy and single crystal X-ray analysis. Complex crystallizes in the monoclinic sp. gr. P2{sub 1}/n, Z = 2. Crystal structure consists of mononuclear units with Fe(II) ion chelated by four S atoms of the two diphenyldithiophosphate ligands in bidentate manner. N atoms from two 4-ethylpyridine ligands are axially coordinated to the Fe(II) atom leading to an octahedral geometry.

  9. Crystal and magnetic structure of TbFe{sub 0.25}Ge{sub 2} compound

    Energy Technology Data Exchange (ETDEWEB)

    Gil, A., E-mail: a.gil@ajd.czest.pl [Faculty of Mathematics and Natural Sciences, Jan Długosz University in Częstochowa, Armii Krajowej 13/15, 42-200 Częstochowa (Poland); Hoser, A. [Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14-109 Berlin (Germany); Penc, B.; Szytuła, A. [M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków (Poland)

    2013-10-15

    The crystal and magnetic structure of polycrystalline TbFe{sub 0.25}Ge{sub 2} sample have been determined. X-ray and neutron diffraction studies indicate that this compound has the orthorhombic CeNiSi{sub 2}-type crystal structure (space group Cmcm). The magnetic ordering, based on the neutron diffraction data in low temperature, is described by two components: a collinear antiferromagnetic G-type and a cosine-wave modulated one. In the collinear G-type structure the Tb magnetic moment is equal to 3.81(5) µ{sub B} and it is parallel to the c-axis. The modulated structure is described by the propagation vector k=(0.460(8), 0, 0.305(1)), the Tb magnetic moment equals 7.75(8) µ{sub B,} lies in b–c and forms an angle 23(2)° with the c-axis. The collinear component decreases to zero at 22.6 K while the modulated one at 190.8 K. - Highlights: • We determine crystal and magnetic structure of TbFe{sub 0.25}Ge{sub 2} compound. • We compare the results with other TbT{sub x}Ge{sub 2} compounds. • We observe the complex magnetic structure in TbFe{sub 0.25}Ge{sub 2} with two components: collinear and cosine-wave modulated. • T (3d) element have got significant influence on the interactions in Tb sublattice.

  10. A novel noncovalent complex of chorismate mutase and DAHP synthase from Mycobacterium tuberculosis: protein purification, crystallization and X-ray diffraction analysis

    International Nuclear Information System (INIS)

    Ökvist, Mats; Sasso, Severin; Roderer, Kathrin; Kast, Peter; Krengel, Ute

    2009-01-01

    Two shikimate-pathway enzymes from M. tuberculosis, the intracellular chorismate mutase (MtCM) and DAHP synthase (MtDS), were produced recombinantly and purified. MtCM was crystallized alone and in complex with MtDS and analyzed by X-ray diffraction. Chorismate mutase catalyzes a key step in the shikimate-biosynthetic pathway and hence is an essential enzyme in bacteria, plants and fungi. Mycobacterium tuberculosis contains two chorismate mutases, a secreted and an intracellular one, the latter of which (MtCM; Rv0948c; 90 amino-acid residues; 10 kDa) is the subject of this work. Here are reported the gene expression, purification and crystallization of MtCM alone and of its complex with another shikimate-pathway enzyme, DAHP synthase (MtDS; Rv2178c; 472 amino-acid residues; 52 kDa), which has been shown to enhance the catalytic efficiency of MtCM. The MtCM–MtDS complex represents the first noncovalent enzyme complex from the common shikimate pathway to be structurally characterized. Soaking experiments with a transition-state analogue are also reported. The crystals of MtCM and the MtCM–MtDS complex diffracted to 1.6 and 2.1 Å resolution, respectively

  11. Copper coordination polymers constructed from thiazole-5-carboxylic acid: Synthesis, crystal structures, and structural transformation

    Energy Technology Data Exchange (ETDEWEB)

    Meundaeng, Natthaya; Rujiwatra, Apinpus [Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Prior, Timothy J., E-mail: t.prior@hull.ac.uk [Chemistry, University of Hull, Kingston upon Hull HU6 7RX (United Kingdom)

    2017-01-15

    We have successfully prepared crystals of thiazole-5-carboxylic acid (5-Htza) (L) and three new thiazole-5-carboxylate-based Cu{sup 2+} coordination polymers with different dimensionality, namely, 1D [Cu{sub 2}(5-tza){sub 2}(1,10-phenanthroline){sub 2}(NO{sub 3}){sub 2}] (1), 2D [Cu(5-tza){sub 2}(MeOH){sub 2}] (2), and 3D [Cu(5-tza){sub 2}]·H{sub 2}O (3). These have been characterized by single crystal X-ray diffraction and thermogravimetry. Interestingly, the 2D network structure of 2 can directly transform into the 3D framework of 3 upon removal of methanol molecules at room temperature. 2 can also undergo structural transformation to produce the same 2D network present in the known [Cu(5-tza){sub 2}]·1.5H{sub 2}O upon heat treatment for 2 h. This 2D network can adsorb water and convert to 3 upon exposure to air. - Highlights: • Rare examples of coordination polymers of thiazole-5-carboxylic acid were prepared. • Non-covalent interactions play a key role on the assembly of the complexes in solid state. • Structural transformation of a 2D framework to a 3D upon removal of methanol is observed.

  12. Effects of the [OC6F5] moiety upon structural geometry: crystal structures of half-sandwich tantalum(V) aryloxide complexes from reaction of Cp*Ta(N(t)Bu)(CH2R)2 with pentafluorophenol.

    Science.gov (United States)

    Cole, Jacqueline M; Chan, Michael C W; Gibson, Vernon C; Howard, Judith A K

    2011-10-01

    The synthesis, chemical and structural characterization of a series of pentamethylcyclopentadienyl (Cp*) tantalum imido complexes and aryloxide derivatives are presented. Specifically, the imido complexes Cp*Ta(N(t)Bu)(CH(2)R)(2), where R = Ph [dibenzyl(tert-butylamido) (η(5)-pentamethylcyclopentadienyl)tantalum(IV) (1)], Me(2)Ph [tert-butylamido)bis(2-methyl-2-phenylpropyl) (η(5)-pentamethylcyclopentadienyl)tantalum(IV) (2)], CMe(3) [(tert-butylamido)bis(2,2-dimethylpropyl) (η(5)-pentamethylcyclopentadienyl)tantalum(IV) (3)], are reported. The crystal structure of (3) reveals α-agostic interactions with the Ta atom. The resulting increase in the tantalum core coordination improves electronic stability. As such it does not react with pentafluorophenol, in contrast to the other two reported imido complexes [(1) and (2)]. Addition of C(6)F(5)OH to (1) yields a dimeric aryl-oxide derivative, [Cp*Ta(CH(2)Ph)(OC(6)H(5))(μ-O)](2) [di-μ-oxido-bis[benzyl(pentafluorophenolato) (η(5)-pentamethylcyclopentadienyl)tantalum(V)] (4)]. Its crystal structure reveals long Ta-O(C(6)H(5)) bonds but short oxo-bridging Ta-O bonds. This is explained by accounting for the fierce electronic competition for the vacant d(π) orbitals of the electrophilic Ta(V) centre. Steric congestion around each metal is alleviated by a large twist angle (77.1°) between the benzyl and pentafluorophenyl ligands and the ordering of each of these groups into stacked pairs. The imido complex (2) reacts with C(6)F(5)OH to produce a mixture of Cp*Ta(OC(6)F(5))(4) [tetrakis(pentafluorophenolato)(η(5)-pentamethylcyclopentadienyl)tantalum(V) (5)] and [Cp*Ta(OC(6)F(5))(2)(μ-O)](2) [di-μ-oxido-bis[bis(pentafluorophenolato)(η(5)-pentamethylcyclopentadienyl)tantalum(V)] (6)]. Steric congestion is offset in both cases by the twisting of its pentafluorophenyl ligands. Particularly strong electronic competition for the empty d(π) metal orbitals in (6) is reflected in its bond geometry, and owes itself to the

  13. Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding

    Directory of Open Access Journals (Sweden)

    Robert Gustafsson

    2018-04-01

    Full Text Available Botulinum neurotoxins (BoNTs are a family of highly dangerous bacterial toxins, with seven major serotypes (BoNT/A-G. Members of BoNTs, BoNT/A1 and BoNT/B1, have been utilized to treat an increasing number of medical conditions. The clinical trials are ongoing for BoNT/A2, another subtype of BoNT/A, which showed promising therapeutic properties. Both BoNT/A1 and BoNT/A2 utilize three isoforms of synaptic vesicle protein SV2 (SV2A, B, and C as their protein receptors. We here present a high resolution (2.0 Å co-crystal structure of the BoNT/A2 receptor-binding domain in complex with the human SV2C luminal domain. The structure is similar to previously reported BoNT/A-SV2C complexes, but a shift of the receptor-binding segment in BoNT/A2 rotates SV2C in two dimensions giving insight into the dynamic behavior of the interaction. Small differences in key residues at the binding interface may influence the binding to different SV2 isoforms, which may contribute to the differences between BoNT/A1 and BoNT/A2 observed in the clinic.

  14. Synthesis, structural characterization and cytotoxic activity of two new organoruthenium(II complexes

    Directory of Open Access Journals (Sweden)

    SANJA GRGURIC-SIPKA

    2008-06-01

    Full Text Available Two new p-cymene ruthenium(II complexes containing as additional ligands N-methylpiperazine ([(η6-p-cymeneRuCl2(CH3NH(CH24NH]PF6, complex 1 or vitamin K3-thiosemicarbazone ([(η6-p-cymeneRuCl2(K3tsc], complex 2 were synthesized starting from [(η6-p-cymene2RuCl2]2 and the corresponding ligand. The complexes were characterized by elemental analysis, IR, electronic absorption and NMR spectroscopy. The X-ray crystal structure determination of complex 1 revealed “piano-stool” geometry. The differences in the cytotoxic activity of the two complexes are discussed in terms of the ligand present.

  15. Crystallization and crystallographic analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA mutant DhaA31 and its complex with 1,2,3-trichloropropane.

    Science.gov (United States)

    Lahoda, Maryna; Chaloupkova, Radka; Stsiapanava, Alena; Damborsky, Jiri; Kuta Smatanova, Ivana

    2011-03-01

    Haloalkane dehalogenases hydrolyze carbon-halogen bonds in a wide range of halogenated aliphatic compounds. The potential use of haloalkane dehalogenases in bioremediation applications has stimulated intensive investigation of these enzymes and their engineering. The mutant DhaA31 was constructed to degrade the anthropogenic compound 1,2,3-trichloropropane (TCP) using a new strategy. This strategy enhances activity towards TCP by decreasing the accessibility of the active site to water molecules, thereby promoting formation of the activated complex. The structure of DhaA31 will help in understanding the structure-function relationships involved in the improved dehalogenation of TCP. The mutant protein DhaA31 was crystallized by the sitting-drop vapour-diffusion technique and crystals of DhaA31 in complex with TCP were obtained using soaking experiments. Both crystals belonged to the triclinic space group P1. Diffraction data were collected to high resolution: to 1.31 Å for DhaA31 and to 1.26 Å for DhaA31 complexed with TCP.

  16. Crystal structure of tris(hydroxylammonium orthophosphate

    Directory of Open Access Journals (Sweden)

    Malte Leinemann

    2015-11-01

    Full Text Available The crystal structure of the title salt, ([H3NOH]+3·[PO4]3−, consists of discrete hydroxylammonium cations and orthophosphate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phosphorus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by intermolecular O—H...O and N—H...O hydrogen bonds into a three-dimensional network. Altogether, one very strong O—H...O, two N—H...O hydrogen bonds of medium strength and two weaker bifurcated N—H...O interactions are observed.

  17. Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N⁴-methyl-3-thiosemicarbazone: crystal structure of a novel sulfur bridged copper(II) box-dimer.

    Science.gov (United States)

    Jayakumar, K; Sithambaresan, M; Aiswarya, N; Kurup, M R Prathapachandra

    2015-03-15

    Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N(4)-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ=0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g||>g⊥>2.0023 and the g values in frozen DMF are consistent with the d(x2-y2) ground state. The thermal stabilities of some of the complexes were also determined. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Crystallization and diffraction patterns of the oxy and cyano forms of the Lucina pectinata haemoglobins complex

    International Nuclear Information System (INIS)

    Ruiz-Martínez, Carlos R.; Nieves-Marrero, Carlos A.; Estremera-Andújar, Rafael A.; Gavira, José A.; González-Ramírez, Luis A.; López-Garriga, Juan; García-Ruiz, Juan M.

    2008-01-01

    The native oxygen-carrier haemoglobins complex (HbII–III) is composed of haemoglobin II (HbII) and haemoglobin III (HbIII), which are found in the ctenidia tissue of the bivalve mollusc Lucina pectinata. This protein complex was isolated and purified from its natural source and crystallized using the vapour-diffusion and capillary counter-diffusion methods. The native oxygen-carrier haemoglobins complex (HbII–III) is composed of haemoglobin II (HbII) and haemoglobin III (HbIII), which are found in the ctenidia tissue of the bivalve mollusc Lucina pectinata. This protein complex was isolated and purified from its natural source and crystallized using the vapour-diffusion and capillary counter-diffusion methods. Oxy and cyano derivatives of the complex crystallized using several conditions, but the best crystals in terms of quality and size were obtained from sodium formate pH 5 using the counter-diffusion method in a single capillary. Crystals of the oxy and cyano complexes, which showed a ruby-red colour and nonsingular prismatic shapes, scattered X-rays to resolution limits of 2.15 and 2.20 Å, respectively, using a 0.886 Å synchrotron-radiation source. The crystals belonged to the tetragonal system, space group P4 2 2 1 2, with unit-cell parameters a = b = 74.07, c = 152.07 and a = b = 73.83, c = 152.49 Å for the oxy and cyano complexes, respectively. The asymmetric unit of both crystals is composed of a single copy of the heterodimer, with Matthew coefficients (V M ) of 3.08 and 3.06 Å 3 Da −1 for the oxy and cyano complexes, respectively, which correspond to a solvent content of approximately 60.0% by volume

  19. Crystal Structure of a Complex of the Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1.

    Science.gov (United States)

    Zhang, Di; Wlodawer, Alexander; Lubkowski, Jacek

    2016-11-20

    The crystal structure of a construct consisting of the FERM and SH2-like domains of the human Janus kinase 1 (JAK1) bound to a fragment of the intracellular domain of the interferon-λ receptor 1 (IFNLR1) has been determined at the nominal resolution of 2.1Å. In this structure, the receptor peptide forms an 85-Å-long extended chain, in which both the previously identified box1 and box2 regions bind simultaneously to the FERM and SH2-like domains of JAK1. Both domains of JAK1 are generally well ordered, with regions not seen in the crystal structure limited to loops located away from the receptor-binding regions. The structure provides a much more complete and accurate picture of the interactions between JAK1 and IFNLR1 than those given in earlier reports, illuminating the molecular basis of the JAK-cytokine receptor association. A glutamate residue adjacent to the box2 region in IFNLR1 mimics the mode of binding of a phosphotyrosine in classical SH2 domains. It was shown here that a deletion of residues within the box1 region of the receptor abolishes stable interactions with JAK1, although it was previously shown that box2 alone is sufficient to stabilize a similar complex of the interferon-α receptor and TYK2. Published by Elsevier Ltd.

  20. Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

    Science.gov (United States)

    Corbett, Michael S P; Mark, Alan E; Poger, David

    2017-02-28

    Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  1. Ultrasmall-angle X-ray scattering analysis of photonic crystal structure

    International Nuclear Information System (INIS)

    Abramova, V. V.; Sinitskii, A. S.; Grigor'eva, N. A.; Grigor'ev, S. V.; Belov, D. V.; Petukhov, A. V.; Mistonov, A. A.; Vasil'eva, A. V.; Tret'yakov, Yu. D.

    2009-01-01

    The results of an ultrasmall-angle X-ray scattering study of iron(III) oxide inverse opal thin films are presented. The photonic crystals examined are shown to have fcc structure with amount of stacking faults varying among the samples. The method used in this study makes it possible to easily distinguish between samples with predominantly twinned fcc structure and nearly perfect fcc stacking. The difference observed between samples fabricated under identical conditions is attributed to random layer stacking in the self-assembled colloidal crystals used as templates for fabricating the inverse opals. The present method provides a versatile tool for analyzing photonic crystal structure in studies of inverse opals made of various materials, colloidal crystals, and three-dimensional photonic crystals of other types.

  2. Scale-free crystallization of two-dimensional complex plasmas: Domain analysis using Minkowski tensors

    Science.gov (United States)

    Böbel, A.; Knapek, C. A.; Räth, C.

    2018-05-01

    Experiments of the recrystallization processes in two-dimensional complex plasmas are analyzed to rigorously test a recently developed scale-free phase transition theory. The "fractal-domain-structure" (FDS) theory is based on the kinetic theory of Frenkel. It assumes the formation of homogeneous domains, separated by defect lines, during crystallization and a fractal relationship between domain area and boundary length. For the defect number fraction and system energy a scale-free power-law relation is predicted. The long-range scaling behavior of the bond-order correlation function shows clearly that the complex plasma phase transitions are not of the Kosterlitz, Thouless, Halperin, Nelson, and Young type. Previous preliminary results obtained by counting the number of dislocations and applying a bond-order metric for structural analysis are reproduced. These findings are supplemented by extending the use of the bond-order metric to measure the defect number fraction and furthermore applying state-of-the-art analysis methods, allowing a systematic testing of the FDS theory with unprecedented scrutiny: A morphological analysis of lattice structure is performed via Minkowski tensor methods. Minkowski tensors form a complete family of additive, motion covariant and continuous morphological measures that are sensitive to nonlinear properties. The FDS theory is rigorously confirmed and predictions of the theory are reproduced extremely well. The predicted scale-free power-law relation between defect fraction number and system energy is verified for one more order of magnitude at high energies compared to the inherently discontinuous bond-order metric. It is found that the fractal relation between crystalline domain area and circumference is independent of the experiment, the particular Minkowski tensor method, and the particular choice of parameters. Thus, the fractal relationship seems to be inherent to two-dimensional phase transitions in complex plasmas. Minkowski

  3. Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment

    International Nuclear Information System (INIS)

    Sugiyama, Shigeru; Nomura, Yusuke; Sakamoto, Taiichi; Kitatani, Tomoya; Kobayashi, Asako; Miyakawa, Shin; Takahashi, Yoshinori; Adachi, Hiroaki; Takano, Kazufumi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Nakamura, Yoshikazu; Matsumura, Hiroyoshi

    2008-01-01

    An RNA aptamer in complex with the human IgG Fc fragment have been crystallized. The stirring technique with a rotary shaker was used to improve the crystals and to ensure that they were of high quality and single, resulting in crystals that diffracted to 2.2 Å resolution. Aptamers, which are folded DNA or RNA molecules, bind to target molecules with high affinity and specificity. An RNA aptamer specific for the Fc fragment of human immunoglobulin G (IgG) has recently been identified and it has been demonstrated that an optimized 24-nucleotide RNA aptamer binds to the Fc fragment of human IgG and not to other species. In order to clarify the structural basis of the high specificity of the RNA aptamer, it was crystallized in complex with the Fc fragment of human IgG1. Preliminary X-ray diffraction studies revealed that the crystals belonged to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 83.7, b = 107.2, c = 79.0 Å. A data set has been collected to 2.2 Å resolution

  4. Synthesis, crystal structure, antibacterial activity and theoretical studies on a novel mononuclear cobalt(II) complex based on 2,4,6-tris(2-pyridyl)-1,3,5-triazine ligand

    Science.gov (United States)

    Maghami, Mahboobeh; Farzaneh, Faezeh; Simpson, Jim; Ghiasi, Mina; Azarkish, Mohammad

    2015-08-01

    A cobalt complex was prepared from CoCl2·6H2O and 2,4,6-tris(2-pyridyl)-1,3,5-triazine (tptz) in methanol and designated as [Co(tptz)(CH3OH)Cl2]·CH3OH·0.5H2O (1). It was characterized by several techniques including TGA analysis and FT-IR, UV-Vis and 1H NMR spectral studies. The crystal structure of 1 was determined by single-crystal X-ray diffraction. The Co(II) metal center in 1 is six coordinated with a distorted octahedral geometry. The tptz ligand is tridentate and coordinates to the cobalt through coplanar nitrogen atoms from the triazine and two pyridyl rings. Two chloride anions and a methanol molecule complete the inner coordination sphere of the metal ion. The optimized geometrical parameters obtained by DFT calculation are in good agreement with single XRD data. The in vitro antibacterial activity of various tptz complexes of Co(II), Ni(II), Cu(II), Mn(II) and Rh(III) were evaluated against Gram-positive (Bacillus subtilis, Staphylococcus aureus and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria. Whereas all complexes exhibited good activity in comparison to standard antibacterial drugs, the inhibitory effects of complexes were found to be more than that of the parent ligand. Overall, the obtained results strongly suggest that the cobalt(II) complex is a suitable candidate for counteracting antibiotic resistant microorganisms.

  5. Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.

    Science.gov (United States)

    Pampa, K J; Lokanath, N K; Girish, T U; Kunishima, N; Rai, V R

    2014-10-24

    UDP-N-acetyl-d-mannosamine dehydrogenase (UDP-d-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-d-mannosamine (UDP-d-ManNAc) to Uridine-diphospho-N-acetyl-d-mannosaminuronic acid (UDP-d-ManNAcA) through twofold oxidation of NAD(+). In order to reveal the structural features of the Pyrococcus horikoshii UDP-d-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-d-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Complex and hierarchical micelle architectures from diblock copolymers using living, crystallization-driven polymerizations.

    Science.gov (United States)

    Gädt, Torben; Ieong, Nga Sze; Cambridge, Graeme; Winnik, Mitchell A; Manners, Ian

    2009-02-01

    Block copolymers consist of two or more chemically distinct polymer segments, or blocks, connected by a covalent link. In a selective solvent for one of the blocks, core-corona micelle structures are formed. We demonstrate that living polymerizations driven by the epitaxial crystallization of a core-forming metalloblock represent a synthetic tool that can be used to generate complex and hierarchical micelle architectures from diblock copolymers. The use of platelet micelles as initiators enables the formation of scarf-like architectures in which cylindrical micelle tassels of controlled length are grown from specific crystal faces. A similar process enables the fabrication of brushes of cylindrical micelles on a crystalline homopolymer substrate. Living polymerizations driven by heteroepitaxial growth can also be accomplished and are illustrated by the formation of tri- and pentablock and scarf architectures with cylinder-cylinder and platelet-cylinder connections, respectively, that involve different core-forming metalloblocks.

  7. Structural insights into SUN-KASH complexes across the nuclear envelope

    Institute of Scientific and Technical Information of China (English)

    Wenjia Wang; Zhaocai Zhou; Zhubing Shi; Shi Jiao; Cuicui Chen; Huizhen Wang; Guoguang Liu; Qiang Wang; Yun Zhao; Mark I Greene

    2012-01-01

    Linker of the nucleoskeleton and the cytoskeleton (LINC) complexes are composed of SUN and KASH domaincontaining proteins and bridge the inner and outer membranes of the nuclear envelope.LINC complexes play critical roles in nuclear positioning,cell polarization and cellular stiffness.Previously,we reported the homotrimeric structure of human SUN2.We have now determined the crystal structure of the human SUN2-KASH complex.In the complex structure,the SUN domain homotrimer binds to three independent "hook"-like KASH peptides.The overall conformation of the SUN domain in the complex closely resembles the SUN domain in its apo state.A major conformational change involves the AA'-loop of KASH-bound SUN domain,which rearranges to form a mini β-sheet that interacts with the KASH peptide.The PPPT motif of the KASH domain fits tightly into a hydrophobic pocket on the homotrimeric interface of the SUN domain,which we termed the BI-pocket.Moreover,two adjacent protomers of the SUN domain homotrimer sandwich the KASH domain by hydrophobic interaction and hydrogen bonding.Mutations of these binding sites disrupt or reduce the association between the SUN and KASH domains in vitro.In addition,transfection of wild-type,but not mutant,SUN2 promotes cell migration in Ovcar-3 cells.These results provide a structural model of the LINC complex,which is essential for additional study of the physical and functional coupling between the cytoplasm and the nucleoplasm.

  8. Shrink, twist, ripple and melt: Studies of frustrated liquid crystals

    Science.gov (United States)

    Fernsler, Jonathan G.

    Complex structures can arise out of a simple system with more than one competing influence on its behavior. The protypical example of this is the two-dimensional triangular lattice Ising model. The ferromagnetic model has two simple degenerate ground states of all spins up or down, but the antiferromagnetic model is a frustrated system. Its geometry does not allow satisfaction of the antiferro condition everywhere, which produces complex ordered structures with dimerization of the spins [1]. Without frustration, the complex structures and phase behavior are lost. All of the topics discussed in this thesis concern smectic liquid crystals. Liquid crystals are perhaps uniquely adept at manifesting frustrated phases. Their combination of periodicity in one or more dimensions allows ordered structures, yet their fluid nature in remaining dimensions allows creation of defects and extraordinarily complex structures in ways that a normal crystal could not tolerate. Liquid crystals contain a huge menagerie of frustrated phases and effects including the polarization modulated [2], vortex lattice [3], twist grain boundary [4], and blue [5] phases, as well as frustrated structures such as cholesteric or SmC* helix unwinding [6], defect lattices in thin films [7], and bend melted grain boundary defects [8], arising from boundary conditions and field effects. In this thesis, we study four liquid crystal systems that show unusual phase behavior or complex structures, deriving from the effects of frustration. Frustration, despite some human prejudices against the word, leaves nature all the more interesting and beautiful.

  9. Crystal structure and solid-state properties of discrete hexa cationic ...

    Indian Academy of Sciences (India)

    Subsequently, weight loss of 33% in two stages from 242 to 691◦C can be assigned to the decomposition of triazole ligands. 3.3 Description of the crystal structure. The solid-state structure of ZnT was unambiguously determined by the single crystal X-ray diffraction tech- nique (figures 2 and 3). Compound ZnT crystallizes in.

  10. Crystal structure and magnetism of UOsAl

    Energy Technology Data Exchange (ETDEWEB)

    Andreev, A.V., E-mail: andreev@fzu.cz [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Daniš, S. [Department of Condensed Matter Physics, Charles University, Ke Karlovu 5, 121 16 Prague (Czech Republic); Šebek, J.; Henriques, M.S.; Vejpravová, J. [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Gorbunov, D.I. [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Dresden High Magnetic Field Laboratory (HLD-EMFL), Helmholtz-Zentrum, Dresden-Rossendorf, D-01314 Dresden (Germany); Havela, L. [Department of Condensed Matter Physics, Charles University, Ke Karlovu 5, 121 16 Prague (Czech Republic)

    2017-04-15

    Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn{sub 2} type, space group P6{sub 3}/mmc, with lattice parameters a=536.4 pm, c=845.3 pm. Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). The compound is a weakly temperature-dependent paramagnet with magnetic susceptibility of ≈1.5*10{sup −8} m{sup 3} mol{sup −1} (at T=2 K), which is slightly higher with magnetic field along the a-axis compared to the c-axis. The Sommerfeld coefficient of electronic specific heat has moderate value of γ=36 mJ mol{sup −1} K{sup −2}. - Highlights: • Crystal structure and magnetic properties were studied on single crystal of UOsAl with hexagonal structure of MgZn{sub 2} type. • Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). • UOsAl has paramagnetic ground state as the compounds with T=Fe and Ru, i.e. 3d and 4d analogues of Os.

  11. Structural studies of lanthanide nitrate-N,N'-dimethyl-N,N'-diphenylpyridine-2,6-dicarboxyamide complexes

    International Nuclear Information System (INIS)

    Fujiwara, Asako; Nakano, Yoshiharu; Yaita, Tsuyoshi; Okuno, Kenji

    2008-01-01

    The tridentate ligand N,N'-dimethyl-N,N'-diphenylpyridine-2,6-dicarboxyamide (DMDPhPDA) and the corresponding lanthanum complex [La(NO 3 ) 3 (DMDPhPDA) 2 ] have been prepared and structurally characterised. The crystal structure of DMDPhPDA shows syn-anti conformation. In the lanthanum complex, two DMDPhPDA molecules coordinated to La(III) in a tridentate fashion and to three nitrate ions in a bidentate fashion make the lanthanum atom 12-coordinate. The crystal structure of [La(NO 3 ) 3 (DMDPhPDA) 2 ] has a C 2 symmetry. The stability constants determined by spectrophotometric titration suggest that [Ln(DMDPhPDA) 2 ] 3+ is the primary product in CH 3 CN solution and [Ln(DMDPhPDA) 3 ] 3+ is difficult to form. However, [Ln(DMDPhPDA) 2 ] 3+ could not be distinguished in 1 H NMR spectra. The 1 H NMR titration results imply that a fast ligand exchange process takes place

  12. Fixation of CO2 in air: Synthesis and crystal structure of a µ3-CO3 ...

    Indian Academy of Sciences (India)

    Unknown

    Fixation of CO2 in air: Synthesis and crystal structure of a ... from the reaction between copper(I) complexes and dioxygen.2,6,7 ... and co-workers from the reaction of [(L2) ..... followed by water dissociation.13h,24 While fixation of CO2 by ...

  13. The effect of temperature and pressure on the crystal structure of piperidine.

    Science.gov (United States)

    Budd, Laura E; Ibberson, Richard M; Marshall, William G; Parsons, Simon

    2015-01-01

    The response of molecular crystal structures to changes in externally applied conditions such as temperature and pressure are the result of a complex balance between strong intramolecular bonding, medium strength intermolecular interactions such as hydrogen bonds, and weaker intermolecular van der Waals contacts. At high pressure the additional thermodynamic requirement to fill space efficiently becomes increasingly important. The crystal structure of piperidine-d11 has been determined at 2 K and at room temperature at pressures between 0.22 and 1.09 GPa. Unit cell dimensions have been determined between 2 and 255 K, and at pressures up to 2.77 GPa at room temperature. All measurements were made using neutron powder diffraction. The crystal structure features chains of molecules formed by NH…N H-bonds with van der Waals interactions between the chains. Although the H-bonds are the strongest intermolecular contacts, the majority of the sublimation enthalpy may be ascribed to weaker but more numerous van der Waals interactions. Analysis of the thermal expansion data in the light of phonon frequencies determined in periodic DFT calculations indicates that the expansion at very low temperature is governed by external lattice modes, but above 100 K the influence of intramolecular ring-flexing modes also becomes significant. The principal directions of thermal expansion are determined by the sensitivity of different van der Waals interactions to changes in distance. The principal values of the strain developed on application of pressure are similarly oriented to those determined in the variable-temperature study, but more isotropic because of the need to minimise volume by filling interstitial voids at elevated pressure. Graphical AbstractThough H-bonds are important interactions in the crystal structure of piperidine, the response to externally-applied conditions are determined by van der Waals interactions.

  14. Synthesis, structures and properties of a series of manganese coordination complexes constructed from dicarboxylic fluorene derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Li Xing, E-mail: lixing@nbu.edu.cn [State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211 (China); Zhao Xiuhua; Bing Yue; Zha Meiqin; Xie Hongzhen; Guo Zhiyong [State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211 (China)

    2013-01-15

    Assembly reactions of 9,9-diethylfluorene-2,7-dicarboxylic acid (H{sub 2}DFDC) and Mn(CH{sub 3}COO){sub 2}{center_dot}4H{sub 2}O or MnCl{sub 2}{center_dot}4H{sub 2}O by tuning of various secondary ligands such as 2,2 Prime -bipyridine (2,2 Prime -bpy), 4,4 Prime -bipyridine (4,4 Prime -bpy) or 1,3-bis(4-pyridyl)propane) (bpp), gave rise to four complexes {l_brace} [Mn{sub 2}(DFDC){sub 2}(DMF){sub 2}]{center_dot}H{sub 2}O{r_brace} {sub n} (1), [Mn(DFDC)(2,2 Prime -bpy)]{sub n} (2), {l_brace} [Mn{sub 2}(DFDC){sub 2}(4,4 Prime -bpy){sub 2}]{center_dot}2CH{sub 3}OH{r_brace} {sub n} (3), and {l_brace} [Mn{sub 4}(DFDC){sub 4}(bpp){sub 2}(CH{sub 3}OH){sub 3} (H{sub 2}O){sub 3}]{center_dot}3(CH{sub 3}OH){center_dot}3(H{sub 2}O){r_brace} {sub n} (4). Single crystal X-ray diffraction analysis reveal that complex 1 is three dimensional structure with rhombic channels filled by guest water molecules; 2 presents a close-packed structure with high thermal stability; 3 exhibits a three dimensional framework with micro-porous channels filled by guest methanol molecules and 4 is a two-dimensional structure. The photoluminescent properties of 1-4 have been studied, respectively, showing that the Mn(II) ions, accessorial organic ligands or crystal structures exert important influences on the photoluminescence emissions of H{sub 2}DFDC ligands. Thermogravimetric analysis show that the complexes have remarkably high thermal stability. Magnetic susceptibility measurements have been finished and discussed for the complexes. - Graphical abstract: Assembly of 9,9-diethylfluorene-2,7-dicarboxylic acid and Mn(II) salts by tuning of various accessorial ligands resulted in four manganese complexes with different topological frameworks. Highlights: Black-Right-Pointing-Pointer Four manganese complexes based on 9,9-diethylfluorene-2,7-dicarboxylic acid were obtained. Black-Right-Pointing-Pointer The complexes were structurally characterized by single-crystal X-ray diffraction. Black

  15. Template Syntheses, Crystal Structures and Supramolecular Assembly of Hexaaza Macrocyclic Copper(II) Complexes

    International Nuclear Information System (INIS)

    Kim, Taehyung; Kim, Ju Chang; Lough, Alan J.

    2013-01-01

    Two new hexaaza macrocyclic copper(II) complexes were prepared by a template method and structurally characterized. In the solid state, they were self-assembled by intermolecular interactions to form the corresponding supramolecules 1 and 2, respectively. In the structure of 1, the copper(II) macrocycles are bridged by a tp ligand to form a macrocyclic copper(II) dimer. The dimer extends its structure by intermolecular forces such as hydrogen bonds and C-H···π interactions, resulting in the formation of a double stranded 1D supramolecule. In 2, the basic structure is a monomeric copper(II) macrocycle with deprotonated imidazole pendants. An undulated 1D hydrogen bonded array is achieved through hydrogen bonds between imidazole pendants and secondary amines, where the imidazole pendants act as a hydrogen bond acceptor. The 1D hydrogen bonded supramolecular chain is supported by C-H···π interactions between the methyl groups of acetonitrile ligands and imidazole pendants of the copper(II) macrocycles. In both complexes, the introduction of imidazoles to the macrocycle as a pendant plays an important role for the formation of supramolecules, where they act as intermolecular hydrogen bond donors and/or acceptors, C-H···π and π-π interactions

  16. Crystallization and preliminary X-ray crystallographic studies of a Lys49-phospholipase A{sub 2} homologue from Bothrops pirajai venom complexed with rosmarinic acid

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Juliana I. dos [Departamento de Física e Biofísica, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Botucatu-SP (Brazil); Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq (Brazil); Santos-Filho, Norival A.; Soares, Andreimar M. [Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq (Brazil); Departamento de Análizes Clínicas, Toxicológicas e Bromatológicas, FCFRP, USP, Ribeirão Preto-SP (Brazil); Fontes, Marcos R. M., [Departamento de Física e Biofísica, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Botucatu-SP (Brazil); Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq (Brazil)

    2010-06-01

    PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A{sub 2} from B. pirajai venom, was cocrystallized with the inhibitor rosmarinic acid from C. verbenacea. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved, indicating a remarkable electronic density for the ligand at the entrance to the hydrophobic channel. PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A{sub 2} from Bothrops pirajai venom, was crystallized in the presence of the inhibitor rosmarinic acid (RA). This is the active compound in the methanolic extract of Cordia verbenacea, a plant that is largely used in Brazilian folk medicine. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved by molecular-replacement techniques, showing electron density that corresponds to RA molecules at the entrance to the hydrophobic channel. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, indicating conformational changes in the structure after ligand binding: the crystals of all apo Lys49-phospholipase A{sub 2} structures belong to space group P3{sub 1}21, while the crystals of complexed structures belong to space groups P2{sub 1} or P2{sub 1}2{sub 1}2{sub 1}.

  17. Models of protein–ligand crystal structures: trust, but verify

    Science.gov (United States)

    Deller, Marc C.

    2015-01-01

    X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

  18. Models of protein-ligand crystal structures: trust, but verify.

    Science.gov (United States)

    Deller, Marc C; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  19. Programmatic conversion of crystal structures into 3D printable files using Jmol

    OpenAIRE

    Scalfani, Vincent F.; Williams, Antony J.; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M.; Liddie, Jahred M.; Bara, Jason E.

    2016-01-01

    Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from...

  20. Crystallization and preliminary crystallographic study of carnosinase CN2 from mice

    Energy Technology Data Exchange (ETDEWEB)

    Yamashita, Tetsuo; Unno, Hideaki; Ujita, Sayuri; Otani, Hiroto; Okumura, Nobuaki; Hashida-Okumura, Akiko; Nagai, Katsuya; Kusunoki, Masami, E-mail: kusunoki@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871 (Japan)

    2006-10-01

    Mouse carnosinase was crystallized in complex with Zn{sup 2+} or Mn{sup 2+} and the complexes are undergoing structure determination by the MAD method. Mammalian tissues contain several histidine-containing dipeptides, of which l-carnosine is the best characterized and is found in various tissues including the brain and skeletal muscles. However, the mechanism for its biosynthesis and degradation have not yet been fully elucidated. Crystallographic study of carnosinase CN2 from mouse has been undertaken in order to understand its enzymatic mechanism from a structural viewpoint. CN2 was crystallized by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant. Crystals were obtained in complex with either Mn{sup 2+} or Zn{sup 2+}. Both crystals of CN2 belong to the monoclinic space group P2{sub 1} and have almost identical unit-cell parameters (a = 54.41, b = 199.77, c = 55.49 Å, β = 118.52° for the Zn{sup 2+} complex crystals). Diffraction data were collected to 1.7 and 2.3 Å for Zn{sup 2+} and Mn{sup 2+} complex crystals, respectively, using synchrotron radiation. Structure determination is ongoing using the multiple-wavelength anomalous diffraction (MAD) method.

  1. Crystallization and preliminary crystallographic study of carnosinase CN2 from mice

    International Nuclear Information System (INIS)

    Yamashita, Tetsuo; Unno, Hideaki; Ujita, Sayuri; Otani, Hiroto; Okumura, Nobuaki; Hashida-Okumura, Akiko; Nagai, Katsuya; Kusunoki, Masami

    2006-01-01

    Mouse carnosinase was crystallized in complex with Zn 2+ or Mn 2+ and the complexes are undergoing structure determination by the MAD method. Mammalian tissues contain several histidine-containing dipeptides, of which l-carnosine is the best characterized and is found in various tissues including the brain and skeletal muscles. However, the mechanism for its biosynthesis and degradation have not yet been fully elucidated. Crystallographic study of carnosinase CN2 from mouse has been undertaken in order to understand its enzymatic mechanism from a structural viewpoint. CN2 was crystallized by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant. Crystals were obtained in complex with either Mn 2+ or Zn 2+ . Both crystals of CN2 belong to the monoclinic space group P2 1 and have almost identical unit-cell parameters (a = 54.41, b = 199.77, c = 55.49 Å, β = 118.52° for the Zn 2+ complex crystals). Diffraction data were collected to 1.7 and 2.3 Å for Zn 2+ and Mn 2+ complex crystals, respectively, using synchrotron radiation. Structure determination is ongoing using the multiple-wavelength anomalous diffraction (MAD) method

  2. Silver(I) complexes of mono- and bidentate N-heterocyclic carbene ligands: synthesis, crystal structures, and in vitro antibacterial and anticancer studies.

    Science.gov (United States)

    Haque, Rosenani A; Choo, Sze Yii; Budagumpi, Srinivasa; Iqbal, Muhammad Adnan; Al-Ashraf Abdullah, Amirul

    2015-01-27

    A series of benzimidazole-based N-heterocyclic carbene (NHC) proligands {1-benzyl-3-(2-methylbenzyl)-benzimidazolium bromide/hexafluorophosphate (1/4), 1,3-bis(2-methylbenzyl)-benzimidazolium bromide/hexafluorophosphate (2/5) and 1,3-bis(3-(2-methylbenzyl)-benzimidazolium-1-ylmethylbenzene dibromide/dihexafluorophosphate (3/6)} has been synthesized by the successive N-alkylation method. Ag complexes {1-benzyl-3-(2-methylbenzyl)-benzimidazol-2-ylidenesilver(I) hexafluorophosphate (7), 1,3-bis(2-methylbenzyl)-benzimidazol-2-ylidenesilver(I) hexafluorophosphate (8) and 1,3-bis(3-(2-methylbenzyl)-benzimidazol-2-ylidene)-1-ylmethylbenzene disilver(I) dihexafluorophosphate (9)} of NHC ligands have been synthesized by the treatment of benzimidazolium salts with Ag2O at mild reaction conditions. Both, NHC proligands and Ag-NHC complexes have been characterized by (1)H and (13)C{(1)H} NMR and FTIR spectroscopy and elemental analysis technique. Additionally, the structure of the NHC proligand 5 and the mononuclear Ag complexes 7 and 8 has been elucidated by the single crystal X-ray diffraction analysis. Both the complexes exhibit the same general structural motif with linear coordination geometry around the Ag centre having two NHC ligands. Preliminary in vitro antibacterial potentials of reported compounds against a Gram negative (Escherichia coli) and a Gram positive (Bacillus subtilis) bacteria evidenced the higher activity of mononuclear silver(I) complexes. The anticancer studies against the human derived colorectal cancer (HCT 116) and colorectal adenocarcinoma (HT29) cell lines using the MTT assay method, revealed the higher activity of Ag-NHC complexes. The benzimidazolium salts 4-6 and Ag-NHC complexes 7-9 displayed the following IC50 values against the HCT 116 and HT29 cell lines, respectively, 31.8 ± 1.9, 15.2 ± 1.5, 4.8 ± 0.6, 10.5 ± 1.0, 18.7 ± 1.6, 1.20 ± 0.3 and 245.0 ± 4.6, 8.7 ± 0.8, 146.1 ± 3.1, 7.6 ± 0.7, 5.5 ± 0.8, 103.0 ± 2.3 μM. Copyright

  3. Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation.

    Science.gov (United States)

    Kim, Kuglae; Cha, Jeong Seok; Cho, Yong-Soon; Kim, Hoyoung; Chang, Nienping; Kim, Hye-Jung; Cho, Hyun-Soo

    2018-04-07

    Dual-specificity tyrosine-regulated kinases (DYRKs) auto-phosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues. The auto-phosphorylation occurs intramolecularly and is a one-off event. DYRK3 is selectively expressed at a high level in hematopoietic cells and attenuates erythroblast development, leading to anemia. In the present study, we determined the crystal structure of the mature form of human DYRK3 in complex with harmine, an ATP competitive inhibitor. The crystal structure revealed a phosphorylation site, residue S350, whose phosphorylation increases the stability of DYRK3 and enhances its kinase activity. In addition, our structural and biochemical assays suggest that the N-terminal auto-phosphorylation accessory domain stabilizes the DYRK3 protein, followed by auto-phosphorylation of the tyrosine of the activation loop, which is important for kinase activity. Finally, our docking analysis provides information for the design of novel and potent therapeutics to treat anemia. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. An unsymmetrical porphyrin and its metal complexes: synthesis, spectroscopy, thermal analysis and liquid crystal properties

    Directory of Open Access Journals (Sweden)

    CHANGFU ZHUANG

    2009-09-01

    Full Text Available The synthesis and characterization of a new unsymmetrical porphyrin liquid crystal, 5-(4-stearoyloxyphenylphenyl-10,15,20-triphenylporphyrin (SPTPPH2 and its transition metal complexes (SPTPPM, M(II = Zn, Fe, Co, Ni, Cu or Mn are reported. Their structure and properties were studied by elemental analysis, and UV–Vis, IR, mass and 1H-HMR spectroscopy. Their luminescent properties were studied by excitation and emission spectroscopy. The quantum yields of the S1 ® S0 fluorescence were measured at room temperature. According to thermal studies, the complexes have a higher thermal stability (no decomposition until 200 °C. Differential scanning calorimetry (DSC data and an optical textural photograph, obtained using a polarizing microscope (POM, indicate that the porphyrin ligand had liquid crystalline character and that it exhibited more than one mesophase and a low-lying phase transition temperature, with transition temperatures of 19.3 and 79.4 °C; the temperature range of the liquid crystal (LC phase of the ligand was 70.1 °C.

  5. Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.

    Science.gov (United States)

    Neelon, Kelly; Roberts, Mary F; Stec, Boguslaw

    2011-12-07

    1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutants. Additionally, we obtained the structure of mIPS with a trapped 5-keto-glucose-6-phosphate intermediate at 2 Å resolution by a novel (to our knowledge) process of activating the crystal at high temperature. A comparison of all of the crystal structures of mIPS described in this work suggests a novel type of catalytic mechanism that relies on the forced atomic proximity of functional groups. The lysine cluster is contained in a small volume in the active site, where random motions of these side chains are responsible for the progress of the complex multistep reaction as well as for the low rate of catalysis. The mechanism requires that functional groups of Lys-274, Lys-278, Lys-306, and Lys-367 assume differential roles in the protonation/deprotonation steps that must occur during the mIPS reaction. This mechanism is supported by the complete loss of activity of the enzyme caused by the Leu-257 mutation to Ala that releases the lysine containment. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Structural Basis for the Interaction of the Golgi-Associated Retrograde Protein (GARP) Complex with the t-SNARE Syntaxin 6

    Science.gov (United States)

    Abascal-Palacios, Guillermo; Schindler, Christina; Rojas, Adriana L; Bonifacino, Juan S.; Hierro, Aitor

    2016-01-01

    Summary The Golgi-Associated Retrograde Protein (GARP) is a tethering complex involved in the fusion of endosome-derived transport vesicles to the trans-Golgi network through interaction with components of the Syntaxin 6/Syntaxin 16/Vti1a/VAMP4 SNARE complex. The mechanisms by which GARP and other tethering factors engage the SNARE fusion machinery are poorly understood. Herein we report the structural basis for the interaction of the human Ang2 subunit of GARP with Syntaxin 6 and the closely related Syntaxin 10. The crystal structure of Syntaxin 6 Habc domain in complex with a peptide from the N terminus of Ang2 shows a novel binding mode in which a di-tyrosine motif of Ang2 interacts with a highly conserved groove in Syntaxin 6. Structure-based mutational analyses validate the crystal structure and support the phylogenetic conservation of this interaction. The same binding determinants are found in other tethering proteins and syntaxins, suggesting a general interaction mechanism. PMID:23932592

  7. Biological Activity and Molecular Structures of Bis(benzimidazole and Trithiocyanurate Complexes

    Directory of Open Access Journals (Sweden)

    Pavel Kopel

    2015-06-01

    Full Text Available 1-(1H-Benzimidazol-2-yl-N-(1H-benzimidazol-2-ylmethylmethanamine (abb and 2-(1H-benzimidazol-2-ylmethylsulfanylmethyl-1H-benzimidazole (tbb have been prepared and characterized by elemental analysis. These bis(benzimidazoles have been further used in combination with trithiocyanuric acid for the preparation of complexes. The crystal and molecular structures of two of them have been solved. Each nickel atom in the structure of trinuclear complex [Ni3(abb3(H2O3(μ-ttc](ClO43·3H2O·EtOH (1, where ttcH3 = trithiocyanuric acid, is coordinated with three N atoms of abb, the N,S donor set of ttc anion and an oxygen of a water molecule. The crystal of [(tbbH2(ttcH22(ttcH3(H2O] (2 is composed of a protonated bis(benzimidazole, two ttcH2 anions, ttcH3 and water. The structure is stabilized by a network of hydrogen bonds. These compounds were primarily synthesized for their potential antimicrobial activity and hence their possible use in the treatment of infections caused by bacteria or yeasts (fungi. The antimicrobial and antifungal activity of the prepared compounds have been evaluated on a wide spectrum of bacterial and yeast strains and clinical specimens isolated from patients with infectious wounds and the best antimicrobial properties were observed in strains after the use of ligand abb and complex 1, when at least 80% growth inhibition was achieved.

  8. A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors

    DEFF Research Database (Denmark)

    Fidom, Kimberley; Isberg, Vignir; Hauser, Alexander Sebastian

    2015-01-01

    and receptor residue pairs, from crystal structure complexes. We describe the procedure to collect a library with more than 250 fragments covering 29 residue positions within the generic transmembrane binding pocket. We describe how the library fragments are recombined and inferred to build pharmacophores...... for new targets. A validating retrospective virtual screening of histamine H1 and H3 receptor pharmacophores yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique advantage that it can be applied to targets for which no (homologous) crystal structures...... or ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element pharmacophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of homology models. Researchers can download the complete fragment library or a subset...

  9. Solving crystal structures with the symmetry minimum function

    International Nuclear Information System (INIS)

    Estermann, M.A.

    1995-01-01

    Unravelling the Patterson function (the auto-correlation function of the crystal structure) (A.L. Patterson, Phys. Rev. 46 (1934) 372) can be the only way of solving crystal structures from neutron and incomplete diffraction data (e.g. powder data) when direct methods for phase determination fail. The negative scattering lengths of certain isotopes and the systematic loss of information caused by incomplete diffraction data invalidate the underlying statistical assumptions made in direct methods. In contrast, the Patterson function depends solely on the quality of the available diffraction data. Simpson et al. (P.G. Simpson et al., Acta Crystallogr. 18 (1965) 169) showed that solving a crystal structure with a particular superposition of origin-shifted Patterson functions, the symmetry minimum function, is advantageous over using the Patterson function alone, for single-crystal X-ray data.This paper describes the extension of the Patterson superposition approach to neutron data and powder data by (a) actively using the negative regions in the Patterson map caused by negative scattering lengths and (b) using maximum entropy Patterson maps (W.I.F. David, Nature 346 (1990) 731). Furthermore, prior chemical knowledge such as bond lengths and angles from known fragments have been included. Two successful structure solutions of a known and a previously unknown structure (M. Hofmann, J. Solid State Chem., in press) illustrate the potential of this new development. ((orig.))

  10. Impact of crystallization on the structure and chemical durability of borosilicate glass

    International Nuclear Information System (INIS)

    Nicoleau, Elodie

    2016-01-01

    This work describes a new approach to help understand the chemical durability of partially crystallized nuclear waste conditioning matrices. Among the studies carried out on nuclear waste deep geological disposal, long term behavior studies have so far been conducted on homogeneous glassy matrices. However, as the crystalline phases may generate modifications in the chemical composition and properties of such matrices, the description and a better understanding of their effects on the chemical durability of waste packages are of primary importance. A protocol to study the durability of heterogeneous model matrices of nuclear interest containing different types of crystalline phases was developed. It is based on a detailed description of the morphology, microstructure and structure of the glassy matrix and crystalline phases, and on the study of various alteration regimes. Three crystal phases that may form when higher concentrations of waste are immobilized in Uranium Oxide type conditioning glasses were studied: alkali and alkaline earth molybdates, rare earth silicates and ruthenium oxide. The results highlight the roles of the composition and the structure of the surrounding glassy matrix as the parameters piloting the alteration kinetics of the partially crystallized glassy matrices. This behavior is identical whatever the nature of the crystalline phases, as long as these phases do not lead to a composition gradient and do not percolate within the glassy matrix. Given these results, a methodology to study partially crystallized matrices with no composition gradient is then suggested. Its key development lies firstly in the evaluation of the behavior of partially crystallized matrices through the experimental study of the residual glassy matrix in various alteration regimes. This methodology may be adapted to the case of new glass formulations with more complex compositions (e.g. highly waste-loaded glass), which may contain crystals formed during cooling

  11. Purification, characterization and crystallization of the F-ATPase from Paracoccus denitrificans.

    Science.gov (United States)

    Morales-Rios, Edgar; Watt, Ian N; Zhang, Qifeng; Ding, Shujing; Fearnley, Ian M; Montgomery, Martin G; Wakelam, Michael J O; Walker, John E

    2015-09-01

    The structures of F-ATPases have been determined predominantly with mitochondrial enzymes, but hitherto no F-ATPase has been crystallized intact. A high-resolution model of the bovine enzyme built up from separate sub-structures determined by X-ray crystallography contains about 85% of the entire complex, but it lacks a crucial region that provides a transmembrane proton pathway involved in the generation of the rotary mechanism that drives the synthesis of ATP. Here the isolation, characterization and crystallization of an integral F-ATPase complex from the α-proteobacterium Paracoccus denitrificans are described. Unlike many eubacterial F-ATPases, which can both synthesize and hydrolyse ATP, the P. denitrificans enzyme can only carry out the synthetic reaction. The mechanism of inhibition of its ATP hydrolytic activity involves a ζ inhibitor protein, which binds to the catalytic F₁-domain of the enzyme. The complex that has been crystallized, and the crystals themselves, contain the nine core proteins of the complete F-ATPase complex plus the ζ inhibitor protein. The formation of crystals depends upon the presence of bound bacterial cardiolipin and phospholipid molecules; when they were removed, the complex failed to crystallize. The experiments open the way to an atomic structure of an F-ATPase complex. © 2015 The Authors.

  12. Crystal structure of tris(1,10-phenanthroline-κ2N,N′iron(II bis[bis(trifluoromethylsulfonylimide] monohydrate

    Directory of Open Access Journals (Sweden)

    Kazunori Teramoto

    2015-01-01

    Full Text Available The crystal structure of the title complex, [Fe(C12H8N23][(CF3SO22N]2·H2O, is constructed by one octahedral [Fe(phen3]2+ (phen = 1,10-phenanthroline cation (point group symmetry 2, two Tf2N− [bis(trifluoromethylsulfonylimide] anions, and one water molecule of crystallization (point group 2. The Fe—N bond lengths are indicative of a d6 low-spin state for the FeII ion in the complex. The dihedral angle between the phen ligands in the cation is 87.64 (6°. The Tf2N− counter-anion is non-coordinating, with the –CF3 groups arranged in a trans fashion with respect to each other, leading to an anti,anti conformation of the –CF3 groups and –SO2N– moieties relative to the S—C bonds. The water molecule of crystallization connects two O atoms of the Tf2N− anions through weak hydrogen bonds. C—H...O hydrogen-bonding interactions are also observed, consolidating the packing of the molecules into a three-dimensional network structure.

  13. Synthesis, crystal structures and spectral properties of 6'-phenyl-2,2'-bipyridine derivatives and their CdLI(2) complexes.

    Science.gov (United States)

    Zhao, Xuesong; Chen, Yanxin; Luo, Junshan; Wang, Hui; Li, Shengli; Zhou, Hongping; Wu, Jieying; Tian, Yupeng

    2014-04-05

    Two novel 6'-phenyl-2,2'-bipyridine ligands (L1, L2) and their CdL(1,2)I2 complexes (1, 2) were synthesized and characterized by elemental analysis, (1)H NMR, IR, MALDI-TOF spectroscopy, and single crystal X-ray diffraction analysis. The results reveal that the central cadmium(II) atom in the complexes was coordinated by two iodide ions and two nitrogen atoms from L1, L2, forming a distorted coordination geometry. The electronic absorption properties of them were investigated on the basis of theoretical calculations (TD-DFT). Copyright © 2013 Elsevier B.V. All rights reserved.

  14. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  15. CCDC 1408042: Experimental Crystal Structure Determination : 6,13-dimesitylpentacene

    KAUST Repository

    Shi, Xueliang

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  16. CCDC 1475929: Experimental Crystal Structure Determination : trimethylammonium tribromo-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  17. CCDC 1475930: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  18. CCDC 1475931: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  19. CCDC 1482638: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

    KAUST Repository

    Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

    2016-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  20. Structure, spectra and phase transition in p-nitroanilinium perchlorate crystal

    Energy Technology Data Exchange (ETDEWEB)

    Marchewka, M.K.; Drozd, M.; Pietraszko, A

    2003-07-25

    The first X-ray diffraction and vibrational spectroscopic analysis of a novel complex between p-nitroaniline and perchloric acid is reported. The structure was solved in 295 K. Room temperature powder infrared and Raman measurements for the p-nitroanilinium perchlorate (1:1) crystals were carried out. The vibrational spectra in the region of internal vibrations of ions corroborates the X-ray data which show that p-nitroaniline molecule is monoprotonated. DSC measurements on powder sample indicate the phase transition point at about 213 and 208 K for heating and cooling, respectively. No detectable signal was observed during powder test for second harmonic generation.

  1. The n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside: Syntheses, crystal structure, physical properties and stability constants of their complexes with Cu(II), Ni(II) and VO(II)

    Science.gov (United States)

    Barabaś, Anna; Madura, Izabela D.; Marek, Paulina H.; Dąbrowska, Aleksandra M.

    2017-11-01

    The structure, conformation and configuration of the n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside (BAra-nPr) were determined by 1H NMR, 13C NMR, and IR spectroscopy, as well as by optical rotation. The crystal structure was confirmed by single-crystal X-ray diffraction studies at room temperature. The compound crystallizes in P21 space group symmetry of the monoclinic system. The molecule has a 4C1 chair conformation with azide group in the equatorial position both in a solution as well as in the crystal. The spatial arrangement of azide group is compared to other previously determined azidosugars. The hydrogen bonds between the hydroxyl group of sugar molecules lead to a ribbon structure observed also for the ethyl homolog. The packing of ribbons is dependent on the alkyl substituent length and with the elongation changes from pseudohexagonal to lamellar. Acidity constants for the n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside (BAra-nPr) in an aqueous solution were evaluated by the spectrophotometric and potentiometric titrations methods. Title compound exhibit blue absorption with the maximum wavelengths in the range of 266 nm and 306 nm. Based on these measurements we showed equilibria existing in a particular solution and a distribution of species which have formed during the titration. We also investigated interactions between Cu(II), Ni(II) and VO(II) and title compound (as ligand L) during complexometric titration. On these bases we identified that in [CuII-BAra-nPr]2+ the ratio of the ligand L to metal ion M(II) was 3:1, while in [NiII-BAra-nPr]2+ and [VOII-BAra-nPr]2+ complexes 2:1 ratios were found. The cumulative stability constants (as log β) occurring in an aqueous solution for the complexes of BAra-nPr with Cu(II), Ni(II) and VO(IV) were 14.57; 11.71 and 4.20, respectively.

  2. Nonlinear coherent structures in granular crystals

    Science.gov (United States)

    Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

    2017-10-01

    The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

  3. Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

    KAUST Repository

    Abe, Yuichiro

    2017-08-15

    Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

  4. Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

    KAUST Repository

    Abe, Yuichiro; Savikhin, Victoria; Yin, Jun; Grimsdale, Andrew C.; Soci, Cesare; Toney, Michael F.; Lam, Yeng Ming

    2017-01-01

    Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

  5. Crystal structure of a mononuclear Ru(II) complex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy-tpy)](.).

    Science.gov (United States)

    Rein, Francisca N; Chen, Weizhong; Scott, Brian L; Rocha, Reginaldo C

    2015-09-01

    We report the structural characterization of [6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine](2,2'-bi-pyridine)-chlorido-ruthenium(II) hexa-fluorido-phosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2'-bi-pyridine (bpy) and the tridendate ligand 6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine (tpy-tpy). The [RuCl(bpy)(tpy-tpy)](+) monocation has a distorted octa-hedral geometry at the central Ru(II) ion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru-N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru-Cl. For tpy-tpy, the mean Ru-N distance involving the outer N atoms trans to each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru-Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy-tpy adopts a trans,trans conformation about the inter-annular C-C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π-π stacking inter-actions based on tpy-tpy. The crystal structure reported here is the first for a tpy-tpy complex of ruthenium.

  6. The production and crystallization of the human leukocyte antigen class II molecules HLA-DQ2 and HLA-DQ8 complexed with deamidated gliadin peptides implicated in coeliac disease

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Kate N.; Reid, Hugh H.; Borg, Natalie A.; Broughton, Sophie E.; Huyton, Trevor [The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800 (Australia); Anderson, Robert P. [Autoimmunity and Transplantation Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria 3050 (Australia); Department of Gastroenterology, The Royal Melbourne Hospital, Grattan Street, Parkville, Victoria 3050 (Australia); McCluskey, James [Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010 (Australia); Rossjohn, Jamie, E-mail: jamie.rossjohn@med.monash.edu.au [The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800 (Australia)

    2007-12-01

    The production and crystallization of human leukocyte antigen class II molecules HLA-DQ2 and HLA-DQ8 in complex with deamidated gliadin peptides is reported. Crystals of HLA-DQ2{sup PQPELPYPQ} diffracted to 3.9 Å, while the HLA-DQ8{sup EGSFQPSQE} crystals diffracted to 2.1 Å, allowing structure determination by molecular replacement. The major histocompatibility complex (MHC) class II molecules HLA-DQ2 and HLA-DQ8 are key risk factors in coeliac disease, as they bind deamidated gluten peptides that are subsequently recognized by CD4{sup +} T cells. Here, the production and crystallization of both HLA-DQ2 and HLA-DQ8 in complex with the deamidated gliadin peptides DQ2 α-I (PQPELPYPQ) and DQ8 α-I (EGSFQPSQE), respectively, are reported.

  7. Syntheses, structural characterization and spectroscopic studies of cadmium(II)-metal(II) cyanide complexes with 4-(2-aminoethyl)pyridine

    Science.gov (United States)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Hökelek, Tuncer

    2017-02-01

    Three new cadmium(II)-metal(II) cyanide complexes, [Cd(4aepy)2(H2O)2][Ni(CN)4] (1), [Cd(4aepy)2(H2O)2][Pd(CN)4] (2) and [Cd(4aepy)2(H2O)2][Pt(CN)4] (3) [4aepy = 4-(2-aminoethyl)pyridine], have been synthesized and characterized by elemental, thermal, FT-IR and Raman spectral analyses. The crystal structures of 1 and 2 have been determined by single crystal X-ray diffraction technique, in which they crystallize in the monoclinic system and C2/c space group. The M(II) [M(II) = Ni(II), Pd(II) and Pt(II)] ions are coordinated with the carbon atoms of the four cyanide groups in the square planar geometries and the [M(CN)4]2- ions act as counter ions. The Cd(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. 3D supramolecular structures of 1 and 2 were occurred by M⋯π and hydrogen bonding (Nsbnd H⋯N and Osbnd H⋯N) interactions. Vibrational assignments of all the observed bands were given and the spectral properties were also supported the crystal structures of the complexes. A possible decompositions of the complexes were investigated in the temperature range 30-800 °C in the static atmosphere.

  8. Characterization of crystals of an antibody-recognition fragment of the cancer differentiation antigen mesothelin in complex with the therapeutic antibody MORAb-009

    International Nuclear Information System (INIS)

    Ma, Jichun; Tang, Wai Kwan; Esser, Lothar; Pastan, Ira; Xia, Di

    2012-01-01

    The therapeutic antibody MORAb-009 disrupts the interaction of mesothelin and the ovarian cancer antigen CA-125. Crystals have been grown of the Fab fragment derived from MORAb-009 and of its complex with an N-terminal fragment of mesothelin. The mesothelin-specific monoclonal antibody MORAb-009 is capable of blocking the binding of mesothelin to CA-125 and displays promising anticancer potential. It is currently undergoing clinical trials. In order to understand the basis of the interaction between MORAb-009 and mesothelin at atomic resolution, both the Fab fragment of MORAb-009 and the complex between the Fab and an N-terminal fragment of mesothelin (residues 7–64) were crystallized. The crystals of the Fab diffracted X-rays to 1.75 Å resolution and had the symmetry of space group P4 1 2 1 2, with unit-cell parameters a = b = 140.6, c = 282.0 Å. The crystals of the mesothelin–Fab complex diffracted to 2.6 Å resolution and belonged to the hexagonal space group P6 4 , with unit-cell parameters a = b = 146.2, c = 80.9 Å. Structural analyses of these molecules are in progress

  9. Crystal structures of orthorhombic, hexagonal, and cubic compounds of the Sm(x)Yb(2−x)TiO5 series

    International Nuclear Information System (INIS)

    Aughterson, Robert D.; Lumpkin, Gregory R.; Reyes, Massey de los; Sharma, Neeraj; Ling, Christopher D.; Gault, Baptiste; Smith, Katherine L.; Avdeev, Maxim; Cairney, Julie M.

    2014-01-01

    A series of single phase compounds with nominal stoichiometry Sm (x) Yb (2−x) TiO 5 (x=2, 1.4, 1, 0.6, and 0) have been successfully fabricated to generate a range of crystal structures covering the most common polymorphs previously discovered in the Ln 2 TiO 5 series (Ln=lanthanides and yttrium). Four of the five samples have not been previously fabricated in bulk, single phase form so their crystal structures are refined and detailed using powder synchrotron and single crystal x-ray diffraction, neutron diffraction and transmission electron microscopy. Based on the phase information from diffraction data, there are four crystal structure types in this series; orthorhombic Pnma, hexagonal P6 3 /mmc, cubic (pyrochlore-like) Fd-3m and cubic (fluorite-like) Fm-3m. The cubic materials show modulated structures with variation between long and short range ordering and the variety of diffraction techniques were used to describe these complex crystal structure types. - Graphical abstract: A high resolution image of the compound Sm 0.6 Yb 1.4 TiO 5 showing contrast from lattice fringes and the corresponding fast Fourier transform (FFT) of the HREM image with pyrochlore related diffraction spots marked “P” and fluorite marked “F”. The crystal is oriented down the [1 1 0] zone axis based on the Fd-3m structure. The ideal crystal structure (no vacancies) of the cubic, pyrochlore-like (Sm 0.6 Yb 1.4 TiO 5 ). - Highlights: • First fabrication of bulk single-phase material with stoichiometry Sm 2 TiO 5 . • Systematic study of crystal structure types within Ln 2 TiO 5 series (Ln=lanthanides). • A novel technique using IFFT of HREM images to study cubic structures

  10. Crystal structure of prethrombin-1

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Zhiwei; Pelc, Leslie A.; Di Cera, Enrico (St. Louis-MED)

    2010-11-15

    Prothrombin is the zymogen precursor of the clotting enzyme thrombin, which is generated by two sequential cleavages at R271 and R320 by the prothrombinase complex. The structure of prothrombin is currently unknown. Prethrombin-1 differs from prothrombin for the absence of 155 residues in the N-terminal domain and is composed of a single polypeptide chain containing fragment 2 (residues 156-271), A chain (residues 272-320), and B chain (residues 321-579). The X-ray crystal structure of prethrombin-1 solved at 2.2-{angstrom} resolution shows an overall conformation significantly different (rmsd = 3.6 {angstrom}) from that of its active form meizothrombin desF1 carrying a cleavage at R320. Fragment 2 is rotated around the y axis by 29{sup o} and makes only few contacts with the B chain. In the B chain, the oxyanion hole is disrupted due to absence of the I16-D194 ion pair and the Na{sup +} binding site and adjacent primary specificity pocket are highly perturbed. A remarkable feature of the structure is that the autolysis loop assumes a helical conformation enabling W148 and W215, located 17 {angstrom} apart in meizothrombin desF1, to come within 3.3 {angstrom} of each other and completely occlude access to the active site. These findings suggest that the zymogen form of thrombin possesses conformational plasticity comparable to that of the mature enzyme and have significant implications for the mechanism of prothrombin activation and the zymogen {yields} protease conversion in trypsin-like proteases.

  11. Photonic Crystal Laser-Driven Accelerator Structures

    International Nuclear Information System (INIS)

    Cowan, Benjamin M.

    2007-01-01

    Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques

  12. Structural and functional insights into the malaria parasite moving junction complex.

    Directory of Open Access Journals (Sweden)

    Brigitte Vulliez-Le Normand

    Full Text Available Members of the phylum Apicomplexa, which include the malaria parasite Plasmodium, share many features in their invasion mechanism in spite of their diverse host cell specificities and life cycle characteristics. The formation of a moving junction (MJ between the membranes of the invading apicomplexan parasite and the host cell is common to these intracellular pathogens. The MJ contains two key parasite components: the surface protein Apical Membrane Antigen 1 (AMA1 and its receptor, the Rhoptry Neck Protein (RON complex, which is targeted to the host cell membrane during invasion. In particular, RON2, a transmembrane component of the RON complex, interacts directly with AMA1. Here, we report the crystal structure of AMA1 from Plasmodium falciparum in complex with a peptide derived from the extracellular region of PfRON2, highlighting clear specificities of the P. falciparum RON2-AMA1 interaction. The receptor-binding site of PfAMA1 comprises the hydrophobic groove and a region that becomes exposed by displacement of the flexible Domain II loop. Mutations of key contact residues of PfRON2 and PfAMA1 abrogate binding between the recombinant proteins. Although PfRON2 contacts some polymorphic residues, binding studies with PfAMA1 from different strains show that these have little effect on affinity. Moreover, we demonstrate that the PfRON2 peptide inhibits erythrocyte invasion by P. falciparum merozoites and that this strong inhibitory potency is not affected by AMA1 polymorphisms. In parallel, we have determined the crystal structure of PfAMA1 in complex with the invasion-inhibitory peptide R1 derived by phage display, revealing an unexpected structural mimicry of the PfRON2 peptide. These results identify the key residues governing the interactions between AMA1 and RON2 in P. falciparum and suggest novel approaches to antimalarial therapeutics.

  13. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Cornaby, Sterling [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Szebenyi, Doletha M. E. [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Smilgies, Detlef-M. [CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Schuller, David J.; Gillilan, Richard; Hao, Quan [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Bilderback, Donald H., E-mail: dhb2@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States)

    2010-01-01

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.

  14. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    International Nuclear Information System (INIS)

    Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

    2010-01-01

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used

  15. Synthesis, crystal growth and characterization of bioactive material: 2-amino-1H-benzo[d]imidazol-3-ium salicylate single crystal-a proton transfer molecular complex

    Science.gov (United States)

    Fathima, K. Saiadali; Anitha, K.

    2017-05-01

    The 1:1 molecular adducts 2-aminobenzimidazolium salicylate (ABIS) single crystal was synthesized and grown from 2-aminobenzimidazole (ABI) as a donor and salicylic acid (SA) as an acceptor. The cell parameter was determined using single crystal X-Ray diffraction method and the complex ABIS belongs to monoclinic system. The spectroscopic studies showed that ABIS crystal was an ion pair complex. The FTIR and Raman spectra showed that the presence of O-H, C=N, C=O vibration which confirms the proton transfer from SA to ABI. The UV-Vis spectrum exhibited a visible band at 359nm for ABIS due to the salicylate anion of the molecule. Further the antimicrobial activity of ABIS complex against Staphylococcus aureus, klebsiella pneumonia, Pseudomonas eruginos and E.coli pathogens was investigated. So the complex molecule inhibits both Gram positive and Gram negative bacterial. It is found that benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of ABIS crystal.

  16. Crystal and molecular structures of thorium and uranium tetrakis(hexafluoroacetonylpyrazolide) complexes

    International Nuclear Information System (INIS)

    Volz, K.; Zalkin, A.; Templeton, D.H.

    1976-01-01

    Triclinic crystals of thorium(IV) and uranium(IV) tetrakis(hexafluoroacetonylpyrazolide) are isostructural, with space group P1 and Z = 2. At 23 0 C for Th(C 6 H 3 ON 2 F 6 ) 4 α = 11.282 (5) A, b = 16.245 (7) A, c = 10.836 (5) A, α = 90.14 (5) 0 , β = 108.75 (5) 0 , and γ = 107.07 (5) 0 . For the uranium compound a = 11.302 (5) A, b = 16.377 (8) A, c = 11.000 (5) A, α = 87.85 (5) 0 , β = 111.02 (5) 0 , and γ = 109.95 (5) 0 . X-ray diffraction data were measured with a scintillation counter, theta-2theta scans, and Mo Kα radiation. For thorium the conventional R value is 0.026 for 2966 unique data with I greater than sigma(I), and for uranium it is 0.027 for 4125 unique data with I greater than sigma(I). The full-matrix least-squares refinement of the 598 parameters of each structure included anisotropic thermal parameters for the 61 nonhydrogen atoms and isotropic ones for the 12 hydrogen atoms. The actinide ion is at the center of an irregular polyhedron of four oxygen and four nitrogen atoms. The average Th-O, Th-N, U-O, and U-N distances are 2.291 (4), 2.637 (5), 2.237 (3), and 2.574 (5) A. The molecules are packed in a manner which resembles cubic closest packing but which is more nearly analogous to the body-centered tetragonal structure of protactinium metal

  17. Synthesis, Crystal Structure and Luminescent Property of Cd (II Complex with N-Benzenesulphonyl-L-leucine

    Directory of Open Access Journals (Sweden)

    Xishi Tai

    2012-09-01

    Full Text Available A new trinuclear Cd (II complex [Cd3(L6(2,2-bipyridine3] [L = N-phenylsulfonyl-L-leucinato] has been synthesized and characterized by elemental analysis, IR and X-ray single crystal diffraction analysis. The results show that the complex belongs to the orthorhombic, space group P212121 with a = 16.877(3 Å, b = 22.875(5 Å, c = 29.495(6 Å, α = β = γ = 90°, V = 11387(4 Å3, Z = 4, Dc= 1.416 μg·m−3, μ = 0.737 mm−1, F (000 = 4992, and final R1 = 0.0390, ωR2 = 0.0989. The complex comprises two seven-coordinated Cd (II atoms, with a N2O5 distorted pengonal bipyramidal coordination environment and a six-coordinated Cd (II atom, with a N2O4 distorted octahedral coordination environment. The molecules form one dimensional chain structure by the interaction of bridged carboxylato groups, hydrogen bonds and p-p interaction of 2,2-bipyridine. The luminescent properties of the Cd (II complex and N-Benzenesulphonyl-L-leucine in solid and in CH3OH solution also have been investigated.

  18. Structural and morphological characterization of fullerite crystals prepared from the vapor phase

    International Nuclear Information System (INIS)

    Haluska, M.; Fejdi, P.; Vybornov, M.; Kuzmany, H.

    1993-01-01

    Crystal structure, habits and surface structures of fullerite crystals prepared from vapor phase were characterized by X-ray analysis, interfacial angle measurements and optical and scanning electron microscopy (SEM). The study of selected C 60 crystals confirmed the fcc structure at room temperature. The crystal habit is determined by two types of morphological faces, namely {100} and {111}. SEM was used for the observation of thermal etched surfaces. (orig.)

  19. Crystal Structure of [Bis(DIMETHYLFORMAMIDE Bis (2,2’-PYRIDYLQUINOLINE Iron (II] Bis-(TETRAPHENYLBORATE

    Directory of Open Access Journals (Sweden)

    Bohari M. Yamin

    2009-11-01

    Full Text Available The goal of this research is to obtain single crystal and structural information of iron(II complex with 2,(2'-pyridylquinoline(pq ligands. The reaction of iron(II salt with 2,(2'-pyridylquinoline ligand and sodiumtetraphenylborate in the molar ratio of 1:3:2 in methanol-N,N-dimethylformamide(dmf solution results in an iron(IIcomplex. The formula of the [Fe(pq2(dmf2](BPh42 complex has been obtained from the iron(II and C, H, N contents.Single crystal of [Fe(pq2(dmf2](BPh42 suitable for X-ray investigation was obtained by evaporation of the complexsolution in N,N-dimethylformamide at room temperature after 24 hours. This compound crystallizes in monoclinicsystem with C2/c space group, a = 27.950(4, b = 14.169(7, c = 17.717(9 Å and b = 105.669(11°. The structureconsist of iron(II is chelated by two pq ligands through the N atoms and two dmf molecules in a six-coordinationenvironment. The charge of the [Fe(pq2(dmf2]2+ cation is balanced by two tetraphenylborate (BPh4- anions.

  20. Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.

    Science.gov (United States)

    Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

    2010-05-01

    The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq-RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq-RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 A, while the type 2 Hfq-RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 A. Diffraction data were collected to a resolution of 2.20 A from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis.