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Sample records for crystallization preliminary x-ray

  1. Crystallization and preliminary X-ray analysis of immunophilin-like FKBP42 from Arabidopsis thaliana

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    Eckhoff, Andreas; Granzin, Joachim [Institut für Biologische Informationsverarbeitung (IBI-2, Biologische Strukturforschung), Forschungszentrum Jülich GmbH, D-52425 Jülich (Germany); Kamphausen, Thilo [Max-Planck-Forschungsstelle für Enzymologie der Proteinfaltung, D-06120 Halle (Germany); Büldt, Georg [Institut für Biologische Informationsverarbeitung (IBI-2, Biologische Strukturforschung), Forschungszentrum Jülich GmbH, D-52425 Jülich (Germany); Schulz, Burkhard [Universität Tübingen, ZMBP, D-72076 Tübingen (Germany); Purdue University, Department of Horticulture and Landscape Architecture, West Lafayette, IN 47907 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institut für Biologische Informationsverarbeitung (IBI-2, Biologische Strukturforschung), Forschungszentrum Jülich GmbH, D-52425 Jülich (Germany)

    2005-04-01

    The crystallization of FKBP42, a multi-domain member of the FK506-binding protein family, from the plant A. thaliana is reported. Two fragments of FKBP42 from Arabidopsis thaliana covering differing lengths of the molecule have been expressed, purified and crystallized. For each construct, crystals belonging to two different space groups were obtained and subjected to preliminary X-ray analysis.

  2. Crystallization and preliminary X-ray analysis of Atg3

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    Yamada, Yuya; Suzuki, Nobuo N.; Fujioka, Yuko [Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812 (Japan); Ichimura, Yoshinobu; Ohsumi, Yoshinori [Department of Cell Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585 (Japan); Inagaki, Fuyuhiko, E-mail: finagaki@pharm.hokudai.ac.jp [Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812 (Japan)

    2006-10-01

    S. cerevisiae Atg3, an E2-like enzyme that mediates the lipidation of Atg8, was crystallized and diffracted to 2.5 Å resolution. Atg3 is an E2-like enzyme that catalyzes the conjugation reaction between Atg8 and phosphatidylethanolamine (PE). The Atg8–PE conjugate is essential for autophagy, the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. Crystals of Saccharomyces cerevisiae Atg3 have been obtained by the sitting-drop vapour-diffusion method using ammonium sulfate and lithium sulfate as precipitants. A native data set was collected from a single crystal to 2.5 Å resolution. The crystals belong to space group P4{sub 1} or P4{sub 3}, with unit-cell parameters a = 59.33, c = 115.22 Å, and are expected to contain one protein molecule per asymmetric unit.

  3. Crystallization and preliminary X-ray analysis of Atg10

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    Yamaguti, Masaya; Suzuki, Nobuo N.; Fujioka, Yuko [Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812 (Japan); Ohsumi, Yoshinori [Division of Molecular Cell Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585 (Japan); Inagaki, Fuyuhiko, E-mail: finagaki@pharm.hokudai.ac.jp [Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812 (Japan)

    2007-05-01

    S. cerevisiae Atg10, an E2-like enzyme that mediates the conjugation reaction between Atg12 and Atg5, was crystallized and diffracted to 2.3 Å resolution. Atg10 is an E2-like enzyme that catalyzes the conjugation reaction between Atg12 and Atg5. The Atg12–Atg5 conjugate is essential for autophagy, the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. Microcrystals of Saccharomyces cerevisiae Atg10 were obtained by the free-interface diffusion method using polyethylene glycol and sodium acetate as precipitants. Using these precipitants, large crystals suitable for data collection were obtained using the sitting-drop vapour-diffusion method. The crystals belong to space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 51.61, c = 256.16 Å, and are estimated to contain two protein molecules per asymmetric unit. A native data set was collected to 2.3 Å resolution from a single crystal.

  4. Crystallization and preliminary X-ray analysis of AzoR (azoreductase) from Escherichia coli

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    Ito, Kosuke [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Nakanishi, Masayuki [Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193 (Japan); Lee, Woo-Cheol; Sasaki, Hiroshi [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Zenno, Shuhei; Saigo, Kaoru [Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kitade, Yukio [Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193 (Japan); Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2005-04-01

    The crystallization and preliminary X-ray analysis of AzoR (azoreductase) have been performed. AzoR (azoreductase), an FMN-dependent NADH-azo compound oxidoreductase from Escherichia coli, has been crystallized in the presence of FMN by the sitting-drop vapour-diffusion method using 2-propanol as a precipitant. AzoR catalyzes the reductive cleavage of azo groups. The crystals were found to diffract X-rays to beyond 1.8 Å resolution using a synchrotron-radiation source. The crystals belonged to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 92.2, c = 51.9 Å. The crystals are expected to contain one subunit of the homodimer in the asymmetric unit (V{sub M} = 2.6 Å{sup 3} Da{sup −1}) and to have a solvent content of 51.6%. Data sets were also collected from heavy-atom derivatives for use in phasing. As a result, crystals soaked in a solution containing K{sub 2}PtCl{sub 4} for 23 d were found to be reasonably isomorphous to the native crystals and the presence of Pt atoms could be confirmed. The data sets from the native crystals and the K{sub 2}PtCl{sub 4}-derivatized crystals are being evaluated for use in structure determination by single isomorphous replacement with anomalous scattering.

  5. Crystallization and preliminary X-ray diffraction analysis of maize aldose reductase

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    Kiyota, Eduardo [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil); Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP (Brazil); Sousa, Sylvia Morais de [Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP (Brazil); Santos, Marcelo Leite dos; Costa Lima, Aline da [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil); Menossi, Marcelo [Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas-SP (Brazil); Yunes, José Andrés [Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas-SP (Brazil); Aparicio, Ricardo, E-mail: aparicio@iqm.unicamp.br [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil)

    2007-11-01

    Preliminary X-ray diffraction studies of apo maize aldose reductase at 2.0 Å resolution are reported. Maize aldose reductase (AR) is a member of the aldo-keto reductase superfamily. In contrast to human AR, maize AR seems to prefer the conversion of sorbitol into glucose. The apoenzyme was crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 47.2, b = 54.5, c = 100.6 Å and one molecule in the asymmetric unit. Synchrotron X-ray diffraction data were collected and a final resolution limit of 2.0 Å was obtained after data reduction. Phasing was carried out by an automated molecular-replacement procedure and structural refinement is currently in progress. The refined structure is expected to shed light on the functional/enzymatic mechanism and the unusual activities of maize AR.

  6. Crystallization and preliminary X-ray studies of mouse centrin1

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    Park, Jung Hee [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Krauss, Norbert [Institut für Biochemie, Charité - Universitätsmedizin Berlin, Monbijoustrasse 2, D-10117 Berlin (Germany); Pulvermüller, Alexander [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Scheerer, Patrick; Höhne, Wolfgang [Institut für Biochemie, Charité - Universitätsmedizin Berlin, Monbijoustrasse 2, D-10117 Berlin (Germany); Giessl, Andreas; Wolfrum, Uwe [Zell- und Matrixbiologie, Institut für Zoologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz (Germany); Hofmann, Klaus Peter, E-mail: kph@charite.de; Ernst, Oliver Peter [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Choe, Hui-Woog, E-mail: kph@charite.de [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Department of Chemistry, College of Natural Science, Chonbuk National University, 561-756 Chonju (Korea, Republic of)

    2005-05-01

    The expression, purification, crystallization and preliminary X-ray diffraction studies of mouse centrin1 are reported. Centrins belong to a family of Ca{sup 2+}-binding EF-hand proteins that play a fundamental role in centrosome duplication and the function of cilia. To shed light on the structure–function relationship of these proteins, mouse centrin1 has been crystallized. The mouse centrin1 has been expressed in Escherichia coli as a GST-centrin fusion protein containing a thrombin protease cleavage site between the fusion partners. Two constructs with different linking-sequence lengths were expressed and purified. Thrombin cleavage yielded functional centrin1 and N-terminally extended centrin1 containing 25 additional residues upstream of its N-terminus. Only N-terminally extended centrin1 (MW ≃ 22 240 Da) could be crystallized at room temperature, using 20–25%(w/v) PEG 1500, 5–10%(v/v) ethylene glycol and 1–2%(v/v) dioxane. Crystals were suitable for X-ray analysis, diffracting to 2.9 Å at 295 K using a rotating-anode X-ray source. They belong to space group C2, with unit-cell parameters a = 60.7, b = 59.6, c = 58.3 Å, β = 109.4°. Assuming the asymmetric cell to be occupied by one centrin1 molecule of 22.2 kDa, the unit cell contains 45% solvent with a crystal volume per protein weight, V{sub M}, of 2.2 Å{sup 3} Da{sup −1}.

  7. Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima

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    Lyashenko, Andrey V.; Zhukhlistova, Nadegda E.; Gabdoulkhakov, Azat G.; Zhukova, Yuliya N. [A. V. Shubnikov Institute of Crystallography, RAS, Leninskiy Prospect 59, 119333 Moscow (Russian Federation); Voelter, Wolfang [Institute of Biochemistry, University of Tuebingen, Physiologisch-Chemisches Institut, Hoppe-Seyler-Strasse 4, 72076 Tuebingen (Germany); Zaitsev, Viatcheslav N. [University of St Andrews, Centre for Biomolecular Sciences, North Haugh, St Andrews, KY16 9ST,Scotland (United Kingdom); Bento, Isabel [Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Apartado 127, Av. Republica, 2781-901 Oeiras (Portugal); Stepanova, Elena V. [A. N. Bakh Institute of Biochemistry, RAS, Leninskiy Prospect 33, 119071 Moscow (Russian Federation); Kachalova, Galina S. [Institute of Theoretical and Experimental Biophysics of RAS, Institutskaya Street 3, 142290 Puschino, Moscow Region (Russian Federation); Koroleva, Ol’ga V. [A. N. Bakh Institute of Biochemistry, RAS, Leninskiy Prospect 33, 119071 Moscow (Russian Federation); Cherkashyn, Evgeniy A.; Tishkov, Vladimir I. [Department of Chemical Enzymology, M. V. Lomonosov Moscow State University, 119992 Moscow (Russian Federation); Lamzin, Victor S.; Schirwitz, Katja [European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22603 Hamburg (Germany); Morgunova, Ekaterina Yu. [A. V. Shubnikov Institute of Crystallography, RAS, Leninskiy Prospect 59, 119333 Moscow (Russian Federation); Betzel, Christian [University of Hamburg, Institute fur Biochemie und Lebensmittelchemie, Department of Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg (Germany); Lindley, Peter F. [Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Apartado 127, Av. Republica, 2781-901 Oeiras (Portugal); Mikhailov, Al’bert M., E-mail: amm@ns.crys.ras.ru [A. V. Shubnikov Institute of Crystallography, RAS, Leninskiy Prospect 59, 119333 Moscow (Russian Federation)

    2006-10-01

    The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented. Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; R{sub free} = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002 ▶) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO{sub 2} substituents.

  8. Crystallization and preliminary X-ray analysis of the RAD protein from Antirrhinum majus

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    Stevenson, Clare E. M.; Burton, Nicolas [Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH (United Kingdom); Costa, Manuela; Nath, Utpal [Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH (United Kingdom); Dixon, Ray A. [Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH (United Kingdom); Coen, Enrico S. [Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH (United Kingdom); Lawson, David M., E-mail: david.lawson@bbsrc.ac.uk [Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH (United Kingdom)

    2005-10-01

    An 8 kDa proteolytic fragment of the A. majus RADIALIS protein was crystallized and X-ray data were collected to 2 Å resolution. Crystals of the RADIALIS protein from Antirrhinum majus were grown by vapour diffusion after limited proteolysis. Mass spectrometry indicated that an 8 kDa fragment had been crystallized corresponding to the predicted MYB DNA-binding domain. X-ray data collected at room temperature were consistent with tetragonal symmetry, whereas data collected at 100 K using crystals cryoprotected by supplementing the mother liquor with ethylene glycol conformed to orthorhombic symmetry. It was subsequently shown that crystals soaked in cryoprotectants that were ‘osmolality-matched’ to the mother liquor retained tetragonal symmetry. Using these crystals, X-ray data were collected in-house to a maximum resolution of 2 Å.

  9. Crystallization and preliminary X-ray diffraction analysis of a chitin-binding domain of hyperthermophilic chitinase from Pyrococcus furiosus

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    Nakamura, Tsutomu; Ishikawa, Kazuhiko; Hagihara, Yoshihisa; Oku, Takashi [National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan); Nakagawa, Atsushi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Inoue, Tsuyoshi [Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ataka, Mitsuo; Uegaki, Koichi, E-mail: k-uegaki@aist.go.jp [National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan)

    2005-05-01

    The expression, purification and preliminary X-ray diffraction studies of a chitin-binding domain of the chitinase from P. furiosus are reported. The crystallization and preliminary X-ray diffraction analysis of the chitin-binding domain of chitinase from a hyperthermophilic archaeon, Pyrococcus furiosus, are reported. The recombinant protein was prepared using an Escherichia coli overexpression system and was crystallized by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected to 1.70 Å resolution. The crystal belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2. The unit-cell parameters were determined to be a = b = 48.8, c = 85.0 Å.

  10. Cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from Thalictrum flavum

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    Pasquo, Alessandra [ENEA Casaccia Research Centre, Dipartimento BIOTEC, Sezione Genetica e Genomica Vegetale, PO Box 2400, I-00100 Rome (Italy); Bonamore, Alessandra; Franceschini, Stefano; Macone, Alberto; Boffi, Alberto; Ilari, Andrea, E-mail: andrea.ilari@uniroma1.it [Istituto di Biologia e Patologia Molecolari, CNR (IBPM) and Department Of Biochemical Sciences, University of Roma ‘La Sapienza’, Piazza Aldo Moro 5, 00179 Roma (Italy); ENEA Casaccia Research Centre, Dipartimento BIOTEC, Sezione Genetica e Genomica Vegetale, PO Box 2400, I-00100 Rome (Italy)

    2008-04-01

    The cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from T. flavum, a protein which catalyzes the first committed step in the biosynthesis of benzylisoquinoline alkaloids, are reported. Norcoclaurine synthase (NCS) catalyzes the condensation of 3,4-dihydroxyphenylethylamine (dopamine) and 4-hydroxyphenylacetaldehyde (4-HPAA) as the first committed step in the biosynthesis of benzylisoquinoline alkaloids in plants. The protein was cloned, expressed and purified. Crystals were obtained at 294 K by the hanging-drop vapour-diffusion method using ammonium sulfate and sodium chloride as precipitant agents and diffract to better than 3.0 Å resolution using a synchrotron-radiation source. The crystals belong to the trigonal space group P3{sub 1}21, with unit-cell parameters a = b = 86.31, c = 118.36 Å. A selenomethionine derivative was overexpressed, purified and crystallized in the same space group. A complete MAD data set was collected at 2.7 Å resolution. The model is under construction.

  11. Purification, crystallization and preliminary X-ray characterization of Bacillus cereus arylamine N-acetyltransferase 3 [(BACCR)NAT3

    DEFF Research Database (Denmark)

    Kubiak, Xavier Jean Philippe; Pluvinage, Benjamin; Li de la Sierra-Gallay, Inès

    2012-01-01

    Arylamine N-acetyltransferases (NATs) are xenobiotic metabolizing enzymes (XMEs) that catalyze the acetylation of arylamines. All functional NATs described to date possess a strictly conserved Cys-His-Asp catalytic triad. Here, the purification, crystallization and preliminary X-ray characterizat......Arylamine N-acetyltransferases (NATs) are xenobiotic metabolizing enzymes (XMEs) that catalyze the acetylation of arylamines. All functional NATs described to date possess a strictly conserved Cys-His-Asp catalytic triad. Here, the purification, crystallization and preliminary X...

  12. Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

    OpenAIRE

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

    2010-01-01

    Nattokinase, a protein found in high levels in the traditional Japanese food natto, has been reported to have high thrombolytic activity. In the present study, the crystallization of native nattokinase and the collection of X-ray diffraction date from a nattokinase crystal to a resolution of 1.74 Å are reported.

  13. Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.

    Science.gov (United States)

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

    2010-12-01

    Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, β=95.2°. Diffraction images were processed to a resolution of 1.74 Å with an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

  14. Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans

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    Nascimento, Alessandro S.; Ferrarezi, Thiago [Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970 (Brazil); Catalano-Dupuy, Daniela L.; Ceccarelli, Eduardo A. [Facultad de Ciencias Bioquímicas y Farmacéuticas, Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario (Argentina); Polikarpov, Igor, E-mail: ipolikarpov@if.sc.usp.br [Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970 (Brazil)

    2006-07-01

    Crystals adequate for X-ray diffraction analysis have been prepared from L. interrogans ferredoxin-NADP{sup +} reductase. Ferredoxin-NADP{sup +} reductase (FNR) is an FAD-containing enzyme that catalyzes electron transfer between NADP(H) and ferredoxin. Here, results are reported of the recombinant expression, purification and crystallization of FNR from Leptospira interrogans, a parasitic bacterium of animals and humans. The L. interrogans FNR crystals belong to a primitive monoclinic space group and diffract to 2.4 Å resolution at a synchrotron source.

  15. Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum

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    Nithianantham, Stanley [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States); Xu, Minghua [Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905 (United States); Wu, Nan [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States); Han, Yiping W., E-mail: ywh2@case.edu [Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905 (United States); Department of Pathology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Shoham, Menachem, E-mail: ywh2@case.edu [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States)

    2006-12-01

    The FadA adhesin from F. nucleatum, which is involved in bacterial attachment and invasion of human oral epithelial cells, has been crystallized in space group P6{sub 1} or P6{sub 5}, and X-ray data have been collected to 1.9 Å resolution. Fusobacterium nucleatum is a Gram-negative anaerobe prevalent in the oral cavity that is associated with periodontal disease, preterm birth and infections in other parts of the human body. The bacteria attach to and invade epithelial and endothelial cells in the gum tissue and elsewhere via a 13.7 kDa adhesin protein FadA (Fusobacterium adhesin A). FadA exists in two forms: the intact form (pre-FadA), consisting of 129 amino acids, and the mature form (mFadA), which lacks an 18-residue signal sequence. Both forms have been expressed in Escherichia coli and purified. mFadA has been crystallized. The crystals belong to the hexagonal space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 59.3, c = 125.7 Å and one molecule per asymmetric unit. The crystals exhibit an unusually high solvent content of 74%. Synchrotron X-ray data have been collected to 1.9 Å. The crystals are suitable for X-ray structure determination. The crystal structure of FadA may provide a basis for the development of therapeutic agents to combat periodontal disease and other infections associated with F. nucleatum.

  16. Purification, crystallization and preliminary X-ray diffraction studies of N-acetylglucosamine-phosphate mutase from Candida albicans

    Energy Technology Data Exchange (ETDEWEB)

    Nishitani, Yuichi; Maruyama, Daisuke; Nonaka, Tsuyoshi; Kita, Akiko [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); Fukami, Takaaki A.; Mio, Toshiyuki; Yamada-Okabe, Hisafumi [Kamakura Research Laboratory, Chugai Pharmaceutical Co. Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530 (Japan); Yamada-Okabe, Toshiko [Department of Hygiene, School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama 236-0004 (Japan); Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Mikazukicho, Sayo-gun, Hyogo 679-5148 (Japan)

    2006-04-01

    Preliminary X-ray diffraction studies on N-acetylglucosamine-phosphate mutase from C. albicans are reported. N-acetylglucosamine-phosphate mutase (AGM1) is an essential enzyme in the synthesis of UDP-N-acetylglucosamine (UDP-GlcNAc) in eukaryotes and belongs to the α-d-phosphohexomutase superfamily. AGM1 from Candida albicans (CaAGM1) was purified and crystallized by the sitting-drop vapour-diffusion method. The crystals obtained belong to the primitive monoclinic space group P2{sub 1}, with unit-cell parameters a = 60.2, b = 130.2, c = 78.0 Å, β = 106.7°. The crystals diffract X-rays to beyond 1.8 Å resolution using synchrotron radiation.

  17. Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain

    Energy Technology Data Exchange (ETDEWEB)

    Shibata, Naoki, E-mail: shibach@sci.u-hyogo.ac.jp [Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248 (Japan); Tomimoto, Yusuke [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502 (Japan); Hanamura, Toru; Yamamoto, Ryo; Ueda, Mai; Ueda, Yasufumi; Mizuno, Nobuhiro; Ogata, Hideaki [Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Komori, Hirofumi; Shomura, Yasuhito [Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248 (Japan); Kataoka, Michihiko; Shimizu, Sakayu [Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502 (Japan); Kondo, Jun [Mitsubishi Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033 (Japan); Yamamoto, Hideki; Kikuchi, Akira [Department of Biochemistry, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8551 (Japan); Higuchi, Yoshiki, E-mail: shibach@sci.u-hyogo.ac.jp [Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248 (Japan)

    2007-06-01

    The DIX domain of rat axin has been purified and crystallized. Crystals diffracted to 2.9 Å resolution using synchrotron radiation. Axin is a negative regulator of the canonical Wnt signalling pathway that mediates the phosphorylation of β-catenin by glycogen synthase kinase 3β. The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, was purified and crystallized by the sitting-drop vapour-diffusion technique using polyethylene glycol 6000 and lithium sulfate as crystallization agents. Crystals belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 91.49, c = 84.92 Å. An X-ray diffraction data set has been collected to a nominal resolution of 2.9 Å.

  18. Crystallization and preliminary X-ray diffraction analysis of HML, a lectin from the red marine alga Hypnea musciformis

    Energy Technology Data Exchange (ETDEWEB)

    Nagano, Celso S.; Gallego del Sol, Francisca [Instituto de Biomedicina de Valencia, CSIC, Valencia (Spain); Cavada, Benildo S.; Nascimento, Kyria Santiago Do [Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE 60451-970 (Brazil); Nunes, Eudismar Vale; Sampaio, Alexandre H. [Laboratorio de Bioquímica Marinha, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, CE 60451-970 (Brazil); Calvete, Juan J., E-mail: jcalvete@ibv.csic.es [Instituto de Biomedicina de Valencia, CSIC, Valencia (Spain)

    2005-11-01

    The crystallization and preliminary X-ray diffraction analysis of a red marine alga lectin isolated from H. musciformis is reported. HML, a lectin from the red marine alga Hypnea musciformis, defines a novel lectin family. Orthorhombic crystals of HML belonging to space group P2{sub 1}2{sub 1}2{sub 1} grew within three weeks at 293 K using the hanging-drop vapour-diffusion method. A complete data set was collected at 2.4 Å resolution. HML is the first marine alga lectin to be crystallized.

  19. Crystallization and preliminary X-ray diffraction studies of arginase from a thermophilic organism Bacillus caldevelox.

    Science.gov (United States)

    Smith, C A; Pratchett, M L; Baker, E N

    1995-09-01

    A thermostable hexameric arginase purified from the extreme thermophile Bacillus caldevelox has been crystallized from Hepes buffer at pH 7.5 in the presence of 12% polyethylene glycol 4000 and 10% 2-propanol, and from cacodylate buffer at pH 7.2 in the presence of 15% 2-propanol and sodium citrate. The latter crystals are more suitable for X-ray diffraction analysis. The crystals are in the orthorhombic space group P2(1)2(1)2(1) with unit-cell dimensions a = 156.3, b = 148.0 and c = 85.4 A. The asymmetric unit contains one hexamer (approximate molecular mass 183 kDa) and has a solvent content of approximately 54%. The crystals diffract to 2.8 A resolution.

  20. Cloning, Expression, Purification, Crystallization and Preliminary X-ray Analysis of Mycoplasma Genitalium Protein MG289

    Energy Technology Data Exchange (ETDEWEB)

    Sippel, K.; Boehlein, S; Sakai, Y; Quirit, J; Agbandje-McKenna, M; Rosser, C; McKenna, R

    2009-01-01

    Mycoplasma genitalium is a human pathogen that is associated with nongonococcal urethritis in men and cervicitis in women. The cloning, expression, purification and crystallization of the protein MG289 from M. genitalium strain G37 are reported here. Crystals of MG289 diffracted X-rays to 2.8 {angstrom} resolution. The crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 49.7, b = 90.9, c = 176.1 {angstrom}. The diffraction data after processing had an overall R{sub merge} of 8.7%. The crystal structure of Cypl, the ortholog of MG289 from M. hyorhinis, has recently been determined, providing a reasonable phasing model; molecular replacement is currently under way.

  1. Purification, crystallization and preliminary X-ray diffraction analysis of royal palm tree (Roystonea regia) peroxidase

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Leandra; Nascimento, Alessandro S. [Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, CEP 13566-590 São Carlos, SP (Brazil); Zamorano, Laura S. [Departamento de Química Física, Facultad de Química, Universidad de Salamanca, 37008 Salamanca (Spain); Shnyrov, Valery L. [Departamento de Bioquímica y Biología Molecular, Facultad de Biología, Universidad de Salamanca, 37007 Salamanca (Spain); Polikarpov, Igor, E-mail: ipolikarpov@if.sc.usp.br [Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, CEP 13566-590 São Carlos, SP (Brazil); Laboratório Nacional de Luz Síncrotron, Campinas, SP (Brazil)

    2007-09-01

    The purification, crystallization, X-ray diffraction data acquisition and molecular-replacement results of royal palm tree (R. regia) peroxidase are described. Royal palm tree peroxidase (RPTP), which was isolated from Roystonea regia leaves, has an unusually high stability that makes it a promising candidate for diverse applications in industry and analytical chemistry [Caramyshev et al. (2005 ▶), Biomacromolecules, 6, 1360–1366]. Here, the purification and crystallization of this plant peroxidase and its X-ray diffraction data collection are described. RPTP crystals were obtained by the hanging-drop vapour-diffusion method and diffraction data were collected to a resolution of 2.8 Å. The crystals belong to the trigonal space group P3{sub 1}21, with unit-cell parameters a = b = 116.83, c = 92.24 Å, and contain one protein molecule per asymmetric unit. The V{sub M} value and solvent content are 4.07 Å{sup 3} Da{sup −1} and 69.8%, respectively.

  2. Overexpression, crystallization and preliminary X-ray crystallographic analysis of phosphopantetheine adenylyltransferase from Enterococcus faecalis

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Ji Yong; Lee, Hyung Ho; Yoon, Hye Jin; Kim, Hyoun Sook; Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2006-11-01

    Phosphopantetheine adenylyltransferase from En. faecalis was crystallized and X-ray diffraction data were collected to 2.70 Å resolution. Phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme A biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from ATP to 4′-phosphopantetheine, yielding 3′-dephospho-CoA and pyrophosphate. Enterococcus faecalis PPAT has been overexpressed in Escherichia coli as a fusion with a C-terminal purification tag and crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium HEPES pH 7.5, 0.8 M sodium dihydrogen phosphate and 0.8 M potassium dihydrogen phosphate. X-ray diffraction data were collected to 2.70 Å at 100 K. The crystals belong to the primitive tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 160.81, c = 225.68 Å. Four copies of the hexameric molecule are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 3.08 Å{sup 3} Da{sup −1} and a solvent content of 60.1%.

  3. Crystallization and preliminary X-ray diffraction analysis of the multidrug efflux transporter NorM from Neisseria gonorrhoeae

    Energy Technology Data Exchange (ETDEWEB)

    Su, Chih-Chia [Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 (United States); Long, Feng [Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011 (United States); McDermott, Gerry [Department of Anatomy, School of Medicine, University of California, San Francisco, CA 94143 (United States); Shafer, William M. [Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322 (United States); Laboratories of Microbial Pathogenesis, VA Medical Center, Decatur, Georgia 30033 (United States); Yu, Edward W., E-mail: ewyu@iastate.edu [Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 (United States); Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011 (United States); Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States)

    2008-04-01

    The multidrug efflux transporter NorM from N. gonorrhoeae has been crystallized and X-ray diffraction data have been collected to a resolution of 6.5 Å. The crystallization and preliminary X-ray data analysis of the NorM multidrug efflux pump produced by Neisseria gonorrhoeae are reported. NorM is a cytoplasmic membrane protein that consists of 459 amino-acid residues. It is a member of the recently classified multidrug and toxic compound extrusion (MATE) family of transporters and recognizes a number of cationic toxic compounds such as ethidium bromide, acriflavin, 2-N-methylellipticinium and ciprofloxacin. Recombinant NorM protein was expressed in Escherichia coli and purified by metal-affinity and gel-filtration chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron light source. The best crystal diffracted anisotropically to 3.8 Å and diffraction data were complete to 6.5 Å resolution. The space group was determined to be C2, with unit-cell parameters a = 81.5, b = 164.4, c = 111.5 Å.

  4. Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Che-Yen [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Miyazaki, Naoyuki [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yamashita, Tetsuo [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Higashiura, Akifumi; Nakagawa, Atsushi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Li, Tian-Cheng; Takeda, Naokazu [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Xing, Li [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Hjalmarsson, Erik; Friberg, Claes [Crystal Research AB, 22370 Lund (Sweden); Liou, Der-Ming [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Sung, Yen-Jen [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Institute of Anatomy and Cell Biology, National Yang-Ming University, 112 Taipei,Taiwan (China); Tsukihara, Tomitake [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Matsuura, Yoshiharu [Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Miyamura, Tatsuo [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Cheng, R. Holland, E-mail: rhch@ucdavis.edu [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden)

    2008-04-01

    A recombinant virus-like particle that is a potential oral hepatitis E vaccine was crystallized. Diffraction data were collected to 8.3 Å resolution and the X-ray structure was phased with the aid of a low-resolution density map determined using cryo-electron microscopy data. Hepatitis E virus (HEV) accounts for the majority of enterically transmitted hepatitis infections worldwide. Currently, there is no specific treatment for or vaccine against HEV. The major structural protein is derived from open reading frame (ORF) 2 of the viral genome. A potential oral vaccine is provided by the virus-like particles formed by a protein construct of partial ORF3 protein (residue 70–123) fused to the N-terminus of the ORF2 protein (residues 112–608). Single crystals obtained by the hanging-drop vapour-diffusion method at 293 K diffract X-rays to 8.3 Å resolution. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 337, b = 343, c = 346 Å, α = β = γ = 90°, and contain one particle per asymmetric unit.

  5. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I., E-mail: inna@ns.crys.ras.ru; Abramchik, Yu. A., E-mail: tostars@mail.ru; Zhukhlistova, N. E., E-mail: ugama@yandex.ru; Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2015-09-15

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6{sub 3}22 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

  6. Crystallization and preliminary X-ray diffraction analysis of human phosphate-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Contreras-Martel, Carlos; Carpentier, Philippe; Morales, Renaud [Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble (France); Renault, Frédérique [Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France); Chesne-Seck, Marie-Laure [Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble (France); Rochu, Daniel; Masson, Patrick [Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France); Fontecilla-Camps, Juan Carlos [Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble (France); Chabrière, Eric, E-mail: eric.chabriere@lcm3b.uhp-nancy.fr [Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France); Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble (France)

    2006-01-01

    The purification, detergent-exchange protocol and crystallization conditions that led to the discovery of HPBP are reported. HPBP is a new human apoprotein that is absent from the genomic database and is the first phosphate transporter characterized in human plasma. Human phosphate-binding protein (HPBP) was serendipitously discovered by crystallization and X-ray crystallography. HPBP belongs to a eukaryotic protein family named DING that is systematically absent from the genomic database. This apoprotein of 38 kDa copurifies with the HDL-associated apoprotein paraoxonase (PON1) and binds inorganic phosphate. HPBP is the first identified transporter capable of binding phosphate ions in human plasma. Thus, it may be regarded as a predictor of phosphate-related diseases such as atherosclerosis. In addition, HPBP may be a potential therapeutic protein for the treatment of such diseases. Here, the purification, detergent-exchange protocol and crystallization conditions that led to the discovery of HPBP are reported.

  7. Crystallization and preliminary X-ray analysis of flap endonuclease 1 (FEN1) from Desulfurococcus amylolyticus.

    Science.gov (United States)

    Mase, Tomoko; Kubota, Keiko; Miyazono, Ken-ichi; Kawarabayasi, Yutaka; Tanokura, Masaru

    2009-09-01

    Flap endonuclease 1 (FEN1) is a structure-specific nuclease that removes 5'-overhanging flaps in DNA repair and removes the RNA/DNA primer during maturation of the Okazaki fragment in lagging-strand DNA replication. FEN1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus was expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with monoammonium dihydrogen phosphate as the precipitant at pH 8.3. X-ray diffraction data were collected to 2.00 A resolution. The space group of the crystal was determined as the primitive hexagonal space group P321, with unit-cell parameters a = b = 103.76, c = 84.58 A. The crystal contained one molecule in the asymmetric unit.

  8. Crystallization and preliminary X-ray analysis of AzoR (azoreductase) from Escherichia coli.

    Science.gov (United States)

    Ito, Kosuke; Nakanishi, Masayuki; Lee, Woo-Cheol; Sasaki, Hiroshi; Zenno, Shuhei; Saigo, Kaoru; Kitade, Yukio; Tanokura, Masaru

    2005-04-01

    AzoR (azoreductase), an FMN-dependent NADH-azo compound oxidoreductase from Escherichia coli, has been crystallized in the presence of FMN by the sitting-drop vapour-diffusion method using 2-propanol as a precipitant. AzoR catalyzes the reductive cleavage of azo groups. The crystals were found to diffract X-rays to beyond 1.8 A resolution using a synchrotron-radiation source. The crystals belonged to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 92.2, c = 51.9 A. The crystals are expected to contain one subunit of the homodimer in the asymmetric unit (VM = 2.6 A3 Da(-1)) and to have a solvent content of 51.6%. Data sets were also collected from heavy-atom derivatives for use in phasing. As a result, crystals soaked in a solution containing K2PtCl4 for 23 d were found to be reasonably isomorphous to the native crystals and the presence of Pt atoms could be confirmed. The data sets from the native crystals and the K2PtCl4-derivatized crystals are being evaluated for use in structure determination by single isomorphous replacement with anomalous scattering.

  9. Expression, Purification, Crystallization And Preliminary X-Ray Studies of Histamine Dehydrogenase From Nocardioides Simplex

    Energy Technology Data Exchange (ETDEWEB)

    Reed, T.M.; Hirakawa, H.; Mure, M.; Scott, E.E.; Limburg, J.

    2009-05-21

    Histamine dehydrogenase (HADH) from Nocardioides simplex catalyzes the oxidative deamination of histamine to produce imidazole acetaldehyde and an ammonium ion. HADH is functionally related to trimethylamine dehydrogenase (TMADH), but HADH has strict substrate specificity towards histamine. HADH is a homodimer, with each 76 kDa subunit containing two redox cofactors: a [4Fe-4S] cluster and an unusual covalently bound flavin mononucleotide, 6-S-cysteinyl-FMN. In order to understand the substrate specificity of HADH, it was sought to determine its structure by X-ray crystallography. This enzyme has been expressed recombinantly in Escherichia coli and successfully crystallized in two forms. Diffraction data were collected to 2.7 {angstrom} resolution at the SSRL synchrotron with 99.7% completeness. The crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 101.14, b = 107.03, c = 153.35 {angstrom}.

  10. Crystallization and preliminary X-ray diffraction analysis of Leishmania major dihydroorotate dehydrogenase.

    Science.gov (United States)

    Cordeiro, Artur T; Feliciano, Patricia R; Nonato, M Cristina

    2006-10-01

    Dihydroorotate dehydrogenases (DHODHs) are flavin-containing enzymes that catalyze the oxidation of L-dihydroorotate to orotate, the fourth step in the de novo pyrimidine nucleotide synthesis pathway. In this study, DHODH from Leishmania major has been crystallized by the vapour-diffusion technique using lithium sulfate as the precipitating agent. The crystals belong to space group P6(1), with unit-cell parameters a = 143.7, c = 69.8 A. X-ray diffraction data were collected to 2.0 A resolution using an in-house rotating-anode generator. Analysis of the solvent content and the self-rotation function indicate the presence of two molecules in the asymmetric unit. The structure has been solved by the molecular-replacement technique.

  11. Crystallization and preliminary X-ray diffraction analysis of human phosphate-binding protein.

    Science.gov (United States)

    Contreras-Martel, Carlos; Carpentier, Philippe; Morales, Renaud; Renault, Frédérique; Chesne-Seck, Marie Laure; Rochu, Daniel; Masson, Patrick; Fontecilla-Camps, Juan Carlos; Chabrière, Eric

    2006-01-01

    Human phosphate-binding protein (HPBP) was serendipitously discovered by crystallization and X-ray crystallography. HPBP belongs to a eukaryotic protein family named DING that is systematically absent from the genomic database. This apoprotein of 38 kDa copurifies with the HDL-associated apoprotein paraoxonase (PON1) and binds inorganic phosphate. HPBP is the first identified transporter capable of binding phosphate ions in human plasma. Thus, it may be regarded as a predictor of phosphate-related diseases such as atherosclerosis. In addition, HPBP may be a potential therapeutic protein for the treatment of such diseases. Here, the purification, detergent-exchange protocol and crystallization conditions that led to the discovery of HPBP are reported.

  12. Crystallization and Preliminary X-ray Diffraction Analysis of motif N from Saccharomyces cerevisiae Dbf4

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, L.; Duong, A; Prasad, A; Duncker, B; Guarne, A

    2009-01-01

    The Cdc7-Dbf4 complex plays an instrumental role in the initiation of DNA replication and is a target of replication-checkpoint responses in Saccharomyces cerevisiae. Cdc7 is a conserved serine/threonine kinase whose activity depends on association with its regulatory subunit, Dbf4. A conserved sequence near the N-terminus of Dbf4 (motif N) is necessary for the interaction of Cdc7-Dbf4 with the checkpoint kinase Rad53. To understand the role of the Cdc7-Dbf4 complex in checkpoint responses, a fragment of Saccharomyces cerevisiae Dbf4 encompassing motif N was isolated, overproduced and crystallized. A complete native data set was collected at 100 K from crystals that diffracted X-rays to 2.75 {angstrom} resolution and structure determination is currently under way.

  13. Crystallization and preliminary X-ray diffraction analysis of restriction endonuclease EcoRII

    Science.gov (United States)

    Karpova, E. A.; Meehan, E.; Pusey, M. L.; Chen, L.

    1999-01-01

    Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal asymmetric unit contains two protein molecules, and self-rotation function analysis shows a pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of crystal diffraction and to search for heavy-atom derivatives are under way.

  14. Expression, crystallization and preliminary X-ray diffraction studies of recombinant Clostridium perfringens β2-toxin

    Energy Technology Data Exchange (ETDEWEB)

    Gurjar, Abhijit A. [Department of Veterinary and Biomedical Science, The Pennsylvania State University (United States); Yennawar, Neela H.; Yennawar, Hemant P. [Macromolecular X-ray Crystallography Facility, The Pennsylvania State University (United States); Rajashankar, Kanagalaghatta R. [Argonne National Laboratory (United States); Hegde, Narasimha V.; Jayarao, Bhushan M., E-mail: bmj3@psu.edu [Department of Veterinary and Biomedical Science, The Pennsylvania State University (United States)

    2007-06-01

    The cloning, expression, purification and crystallization of recombinant Clostridium perfringens β2-toxin is described. The crystals diffracted to 2.9 Å resolution. Clostridium perfringens is a Gram-positive sporulating anaerobic bacterium that is responsible for a wide spectrum of diseases in animals, birds and humans. The virulence of C. perfringens is associated with the production of several enterotoxins and exotoxins. β2-toxin is a 28 kDa exotoxin produced by C. perfringens. It is implicated in necrotic enteritis in animals and humans, a disease characterized by a sudden acute onset with lethal hemorrhagic mucosal ulceration. The recombinant expression, purification and crystallization of β2-toxin using the batch-under-oil technique are reported here. Native X-ray diffraction data were obtained to 2.9 Å resolution on a synchrotron beamline at the F2 station at Cornell High Energy Synchrotron Source (CHESS) using an ADSC Quantum-210 CCD detector. The crystals belong to space group R3, with a dimer in the asymmetric unit; the unit-cell parameters are a = b = 103.71, c = 193.48 Å, α = β = 90, γ = 120° using the hexagonal axis setting. A self-rotation function shows that the two molecules are related by a noncrystallographic twofold axis with polar angles ω = 90.0, ϕ = 210.3°.

  15. The cloning, crystallization and preliminary X-ray analysis of XC2113, a YaeQ protein from Xanthomonas campestris

    Energy Technology Data Exchange (ETDEWEB)

    Chio, Kuo-Cheng; Chin, Ko-Hsin [Institute of Biochemistry, National Chung-Hsing University, Taichung 40227,Taiwan (China); Gao, Fei Philip [Florida State University, Tallahassee, FL 32310 (United States); Lyu, Ping-Chiang [Department of Life Science, National Tsing Hua University, Hsin-Chu,Taiwan (China); Shr, Hui-Lin; Wang, Andrew H.-J. [Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei,Taiwan (China); Core Facility for Protein Crystallography, Academia Sinica, Nankang, Taipei,Taiwan (China); Chou, Shan-Ho, E-mail: shchou@nchu.edu.tw [Institute of Biochemistry, National Chung-Hsing University, Taichung 40227,Taiwan (China)

    2006-10-01

    A YaeQ protein from the plant pathogen X. campestris pv. campestris has been overexpressed in E. coli, purified and crystallized. The crystals diffracted well to a resolution of 1.28 Å. Xanthomonas campestris is a Gram-negative bacterium that is phytopathogenic to cruciferous plants and causes worldwide agricultural loss. It is therefore important to identify potential pathogenic factors involved in this plant disease. Here, the cloning, expression, crystallization and preliminary X-ray analysis of XC2113, a YaeQ protein possibly involved in the production of virulence factors in Xanthomonas campestris pathovar campestris, are reported. The XC2113 crystals diffracted well to a resolution of at least 1.28 Å. They are orthorhombic and belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 32.86, b = 62.69, c = 79.96 Å.

  16. Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional α-amylase/subtilisin inhibitor from Oryza sativa

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yi-Hung [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Peng, Wen-Yan [Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Huang, Yen-Chieh [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Guan, Hong-Hsiang; Hsieh, Ying-Cheng [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Chang, Tschining [Department of Hospitality Management, Nan Jeon Institute of Technology, Yen-Shui, Tainan 73746,Taiwan (China); Chen, Chun-Jung, E-mail: cjchen@nsrrc.org.tw [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China)

    2006-08-01

    The crystallization of rice α-amylase/subtilisin bifunctional inhibitor is reported. Rice bifunctional α-amylase/subtilisin inhibitor (RASI) can inhibit both α-amylase from larvae of the red flour beetle (Tribolium castaneum) and subtilisin from Bacillus subtilis. The synthesis of RASI is up-regulated during the late milky stage in developing seeds. The 8.9 kDa molecular-weight RASI from rice has been crystallized using the hanging-drop vapour-diffusion method. According to 1.81 Å resolution X-ray diffraction data from rice RASI crystals, the crystal belongs to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 79.99, b = 62.95, c = 66.70 Å. Preliminary analysis indicates two RASI molecules in an asymmetric unit with a solvent content of 44%.

  17. Crystallization and preliminary X-ray studies of azoreductases from Bacillus sp. B29

    Science.gov (United States)

    Ogata, Daiki; Ooi, Toshihiko; Fujiwara, Takaaki; Taguchi, Seiichi; Tanaka, Isao; Yao, Min

    2010-01-01

    Azoreductases from Bacillus sp. B29 are NADH-dependent flavoenzymes which contain a flavin mononucleotide (FMN) as a prosthetic group and exist as homodimers composed of 23 kDa subunits. These enzymes catalyze the reductive degradation of various azo compounds by a ping-pong mechanism. In order to determine the structure–function relationship of the azo-dye reduction mechanism, an X-ray crystallographic study of azoreductases was performed. Selenomethionine-labelled AzrA (SeMet-AzrA) and AzrC were crystallized by the hanging-drop vapour-diffusion method. A crystal of SeMet-AzrA diffracted to 2.0 Å resolution and was determined to belong to space group P212121, with unit-cell parameters a = 56.9, b = 69.0, c = 105.4 Å. The native crystals of AzrC belonged to space group C2, with unit-cell parameters a = 192.0, b = 56.6, c = 105.5 Å, β = 115.7°, and diffracted to 2.21 Å resolution. PMID:20445244

  18. Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, Wanius, E-mail: wanius@if.sc.usp.br [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Travensolo, Regiane F. [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Rodrigues, Nathalia C.; Muniz, João R. C. [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Caruso, Célia S. [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Lemos, Eliana G. M. [Laboratório de Bioquímica de Microrganismos e de Plantas, Departamento de Tecnologia, UNESP, Jaboticabal (Brazil); Araujo, Ana Paula U. [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Carrilho, Emanuel, E-mail: wanius@if.sc.usp.br [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil)

    2008-02-01

    Glutathione S-transferase from X. fastidiosa (xfGST) has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.23 Å. Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 Å, α = 63.45, β = 80.66, γ = 94.55°. xfGST crystals diffracted to 2.23 Å resolution on a rotating-anode X-ray source.

  19. Crystallization and preliminary X-ray crystallographic analysis of Sclerotium rolfsii lectin.

    Science.gov (United States)

    Leonidas, Demetres D; Swamy, Bale M; Bhat, Anuradha G; Inamdar, Shashikala R; Kosmopoulou, Magda N; Chrysina, Evangelia D; Oikonomakos, Nikos G

    2003-02-01

    Sclerotium rolfsii lectin (SRL), from the soil-borne phytopathogenic fungus S. rolfsii, has been crystallized. SRL crystals were grown by the hanging-drop vapour-diffusion method using an MPD-ammonium acetate mixture in Tris-HCl buffer pH 8.5. A complete data set from a single crystal at 100 K was collected to 1.1 A resolution using synchrotron radiation. Preliminary crystallographic analysis showed that the crystals belong to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 99.81, c = 63.99 A and two molecules per asymmetric unit.

  20. Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5

    Energy Technology Data Exchange (ETDEWEB)

    DiMattia, Michael; Govindasamy, Lakshmanan; Levy, Hazel C.; Gurda-Whitaker, Brittney; Kalina, Amy [Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610 (United States); Kohlbrenner, Erik [Division of Cell and Molecular Therapy, University of Florida, Gainesville, FL 32610 (United States); Chiorini, John A. [GTTB, NIDCR, National Institutes of Health, Bethesda, MD 20892 (United States); McKenna, Robert [Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610 (United States); Muzyczka, Nicholas [Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610 (United States); Zolotukhin, Sergei [Division of Cell and Molecular Therapy, University of Florida, Gainesville, FL 32610 (United States); Agbandje-McKenna, Mavis, E-mail: mckenna@ufl.edu [Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610 (United States)

    2005-10-01

    The production, purification, crystallization and preliminary crystallographic analysis of empty adeno-associated virus serotype 5 capsids are reported. Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Å resolution using synchrotron radiation and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Å. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.

  1. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of a cyclophilin A-like protein from Piriformospora indica

    OpenAIRE

    Bhatt, Harshesh; Trivedi, Dipesh Kumar; Pal, Ravi Kant; Johri, Atul Kumar; Tuteja, Narendra; Bhavesh, Neel Sarovar

    2012-01-01

    Cyclophin A like protein from Piriformospora indica involved in salt-stress tolerance was cloned, overexpressed, purified and crystallized. The crystals obtained diffracted X-rays to 2 Å resolution and belonged to space group C2221.

  2. Crystallization and preliminary X-ray diffraction analysis of the multidrug efflux transporter NorM from Neisseria gonorrhoeae

    Energy Technology Data Exchange (ETDEWEB)

    Su, C.C.; Long, F.; McDermott, G.; Shafer, W.M.; Yu, E.W. (Emory-MED); (UCSF); (Iowa State)

    2008-06-03

    The crystallization and preliminary X-ray data analysis of the NorM multidrug efflux pump produced by Neisseria gonorrhoeae are reported. NorM is a cytoplasmic membrane protein that consists of 459 amino-acid residues. It is a member of the recently classified multidrug and toxic compound extrusion (MATE) family of transporters and recognizes a number of cationic toxic compounds such as ethidium bromide, acriflavin, 2-N-methylellipticinium and ciprofloxacin. Recombinant NorM protein was expressed in Escherichia coli and purified by metal-affinity and gel-filtration chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron light source. The best crystal diffracted anisotropically to 3.8 {angstrom} and diffraction data were complete to 6.5 {angstrom} resolution. The space group was determined to be C2, with unit-cell parameters a = 81.5, b = 164.4, c = 111.5 {angstrom}.

  3. Purification, crystallization and preliminary X-ray crystallographic analysis of chitinase from Bacillus cereus NCTU2

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Chueh-Yuan [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Wu, Yue-Jin [Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010,Taiwan (China); Hsieh, Yin-Cheng; Guan, Hong-Hsiang [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Tsai, Huei-Ju [Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010,Taiwan (China); Lin, Yi-Hung; Huang, Yen-Chieh; Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Li, Yaw-Kuen, E-mail: ykl@cc.nctu.edu.tw [Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010,Taiwan (China); Chen, Chun-Jung, E-mail: ykl@cc.nctu.edu.tw [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China)

    2006-09-01

    The crystallization of B. cereus chitinase is reported. Chitinases (EC 3.2.1.14) are found in a broad range of organisms, including bacteria, fungi and higher plants, and play different roles depending on their origin. A chitinase from Bacillus cereus NCTU2 (ChiNCTU2) capable of hydrolyzing chitin as a carbon and nitrogen nutrient has been identified as a member of the family 18 glycoside hydrolases. ChiNCTU2 of molecular weight 36 kDa has been crystallized using the hanging-drop vapour-diffusion method. According to the diffraction of chitinase crystals at 1.10 Å resolution, the crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 50.79, b = 48.79, c = 66.87 Å, β = 99.31°. Preliminary analysis indicates there is one chitinase molecule in the asymmetric unit, with a solvent content of 43.4%.

  4. Crystallization and preliminary X-ray diffraction analysis of West Nile virus

    Energy Technology Data Exchange (ETDEWEB)

    Kaufmann, Barbel; Plevka, Pavel; Kuhn, Richard J.; Rossmann, Michael G. (Purdue)

    2010-05-25

    West Nile virus, a human pathogen, is closely related to other medically important flaviviruses of global impact such as dengue virus. The infectious virus was purified from cell culture using polyethylene glycol (PEG) precipitation and density-gradient centrifugation. Thin amorphously shaped crystals of the lipid-enveloped virus were grown in quartz capillaries equilibrated by vapor diffusion. Crystal diffraction extended at best to a resolution of about 25 {angstrom} using synchrotron radiation. A preliminary analysis of the diffraction images indicated that the crystals had unit-cell parameters a {approx_equal} b {approx_equal} 480 {angstrom}, {gamma} = 120{sup o}, suggesting a tight hexagonal packing of one virus particle per unit cell.

  5. Production, Purification, Crystallization and Preliminary X-ray Structural Studies of Adeno-Associated Virus Serotype 5

    Energy Technology Data Exchange (ETDEWEB)

    DiMattia,M.; Govindasamy, L.; Levy, H.; Whitaker-Gurda, B.; Kohlbrenner, E.; Chiorini, J.; McKenna, R.; Muzyczka, N.; Zolotukhin, S.; Agbandje-McKenna, M.

    2005-01-01

    Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Angstroms resolution using synchrotron radiation and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Angstroms. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.

  6. Crystallization and preliminary X-ray analysis of Leishmania major glyoxalase I

    Energy Technology Data Exchange (ETDEWEB)

    Ariza, Antonio; Vickers, Tim J.; Greig, Neil; Fairlamb, Alan H.; Bond, Charles S., E-mail: c.s.bond@dundee.ac.uk [Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH,Scotland (United Kingdom)

    2005-08-01

    The detoxification enzyme glyoxalase I from L. major has been crystallized. Preliminary molecular-replacement calculations indicate the presence of three glyoxalase I dimers in the asymmetric unit. Glyoxalase I (GLO1) is a putative drug target for trypanosomatids, which are pathogenic protozoa that include the causative agents of leishmaniasis. Significant sequence and functional differences between Leishmania major and human GLO1 suggest that it may make a suitable template for rational inhibitor design. L. major GLO1 was crystallized in two forms: the first is extremely disordered and does not diffract, while the second, an orthorhombic form, produces diffraction to 2.0 Å. Molecular-replacement calculations indicate that there are three GLO1 dimers in the asymmetric unit, which take up a helical arrangement with their molecular dyads arranged approximately perpendicular to the c axis. Further analysis of these data are under way.

  7. Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Jagadeesan, G. [Presidency College, Chennai 600 005 (India); Malathy, P.; Gunasekaran, K. [University of Madras, Chennai 600 025 (India); Harikrishna Etti, S. [GKM College of Engineering and Technology, Kamaraj Salai, Chennai 600 063 (India); Aravindhan, S., E-mail: aravindhanpresidency@gmail.com [Presidency College, Chennai 600 005 (India)

    2014-10-25

    The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

  8. Thermostable multicopper oxidase from Thermusthermophilus HB27: crystallization and preliminaryX-ray diffraction analysis of apo and holo forms

    Energy Technology Data Exchange (ETDEWEB)

    Serrano-Posada H.; Stojanoff V.; Valderrama B.; Rudino-Pinera E.

    2011-09-17

    A thermostable multicopper oxidase from Thermus thermophilus HB27 (Tth-MCO) was successfully crystallized using the sitting-drop and hanging-drop vapour-diffusion methods. Crystallization conditions and preliminary X-ray diffraction data to 1.5 {angstrom} resolution obtained using synchrotron radiation at 100 K are reported. The crystals belonged to space group C222{sub 1}, with unit-cell parameters a = 93.6, b = 110.3, c = 96.3 {angstrom}. A monomer in the asymmetric unit yielded a Matthews coefficient (V{sub M}) of 2.60 {angstrom}{sup 3} Da{sup -1} and a solvent content of 53%. An inactive enzyme form, apo-Tth-MCO, was also crystallized and diffraction data were collected to 1.7 {angstrom} resolution. In addition, a second inactive form of the enzyme, Hg-Tth-MCO, was obtained by soaking apo-Tth-MCO crystals with mercury(II) chloride and data were collected to a resolution of 1.7 {angstrom}.

  9. Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase from Juglans regia (jrPPO1)

    Energy Technology Data Exchange (ETDEWEB)

    Zekiri, Florime; Bijelic, Aleksandar; Molitor, Christian; Rompel, Annette, E-mail: annette.rompel@univie.ac.at [Universität Wien, Althanstrasse 14, 1090 Wien (Austria)

    2014-05-28

    The crystallization and preliminary X-ray crystallographic analysis of a plant PPO exhibiting monophenolase activity from J. regia (jrPPO1) in its active form (Asp{sup 101}–Arg{sup 445}) are reported. Tyrosinase is a type 3 copper enzyme that catalyzes the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones, which are precursors for the biosynthesis of melanins. The first plant tyrosinase from walnut leaves (Juglans regia) was purified to homogeneity and crystallized. During the purification, two forms of the enzyme differing only in their C-termini [jrPPO1(Asp{sup 101}–Pro{sup 444}) and jrPPO1(Asp{sup 101}–Arg{sup 445})] were obtained. The most abundant form jrPPO1(Asp{sup 101}–Arg{sup 445}), as described in Zekiri et al. [Phytochemistry (2014 ▶), 101, 5–15], was crystallized, resulting in crystals that belonged to space group C121, with unit-cell parameters a = 115.56, b = 91.90, c = 86.87 Å, α = 90, β = 130.186, γ = 90°, and diffracted to 2.39 Å resolution. Crystals were only obtained from solutions containing at least 30% polyethylene glycol 5000 monomethyl ether in a close-to-neutral pH range.

  10. Crystallization and preliminary X-ray diffraction analysis of Sfh3, a member of the Sec14 protein superfamily

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jihui; Schaaf, Gabriel; Bankaitis, Vytas A.; Ortlund, Eric A.; Pathak, Manish C. (Emory-MED); (UNC)

    2012-03-26

    Sec14 is the major phosphatidylinositol (PtdIns)/phosphatidylcholine (PtdCho) transfer protein in the yeast Saccharomyces cerevisiae and is the founding member of the Sec14 protein superfamily. Recent functional data suggest that Sec14 functions as a nanoreactor for PtdCho-regulated presentation of PtdIns to PtdIns kinase to affect membrane trafficking. Extrapolation of this concept to other members of the Sec14 superfamily suggests a mechanism by which a comprehensive cohort of Sec14-like nanoreactors sense correspondingly diverse pools of lipid metabolites. In turn, metabolic information is translated to signaling circuits driven by phosphoinositide metabolism. Sfh3, one of five Sec14 homologs in yeast, exhibits several interesting functional features, including its unique localization to lipid particles and microsomes. This localization forecasts novel regulatory interfaces between neutral lipid metabolism and phosphoinositide signaling. To launch a detailed structural and functional characterization of Sfh3, the recombinant protein was purified to homogeneity, diffraction-quality crystals were produced and a native X-ray data set was collected to 2.2 {angstrom} resolution. To aid in phasing, SAD X-ray diffraction data were collected to 1.93 {angstrom} resolution from an SeMet-labeled crystal at the Southeast Regional Collaborative Access Team at the Advanced Photon Source. Here, the cloning and purification of Sfh3 and the preliminary diffraction of Sfh3 crystals are reported, enabling structural analyses that are expected to reveal novel principles governing ligand binding and functional specificity for Sec14-superfamily proteins.

  11. Crystallization and preliminary X-ray diffraction analysis of a protease inhibitor from the haemolymph of the Indian tasar silkworm Antheraea mylitta

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Sobhan [Department of Biotechnology, Indian Institute of Technology, Kharagpur (India); Aravind, Penmatsa [Centre for Cellular and Molecular Biology, Hyderabad (India); Madhurantakam, Chaithanya; Ghosh, Ananta Kumar [Department of Biotechnology, Indian Institute of Technology, Kharagpur (India); Sankaranarayanan, Rajan, E-mail: sankar@ccmb.res.in [Centre for Cellular and Molecular Biology, Hyderabad (India); Das, Amit Kumar, E-mail: sankar@ccmb.res.in [Department of Biotechnology, Indian Institute of Technology, Kharagpur (India)

    2006-07-01

    The crystallization and preliminary X-ray crystallographic analysis of a protease inhibitor from the haemolymph of the Indian tasar silk worm A. mylitta is reported. A protein with inhibitory activity against fungal proteases was purified from the haemolymph of the Indian tasar silkworm Antheraea mylitta and was crystallized using the hanging-drop vapour-diffusion method. Polyethylene glycol 3350 was used as a precipitant. Crystals belonged to space group P6{sub 3}22, with unit-cell parameters a = b = 60.6, c = 85.1 Å. X-ray diffraction data were collected and processed to a maximum resolution of 2.1 Å.

  12. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Vibha [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Gupta, Rakesh K. [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi 110021 (India); Khare, Garima [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Salunke, Dinakar M. [National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 (India); Tyagi, Anil K., E-mail: aniltyagi@south.du.ac.in [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India)

    2008-05-01

    The cloning, purification and crystallization of a bacterioferritin from M. tuberculosis together with preliminary X-ray characterization of its crystals are reported. Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein product was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 Å resolution and belonged to space group P4{sub 2}, with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 Å.

  13. 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°.

  14. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Xiong-Zhuo [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Li, Lan-Fen; Su, Xiao-Dong [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Zhao, XiaoJun, E-mail: zhaoxj@scu.edu.cn [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); Liang, Yu-He, E-mail: zhaoxj@scu.edu.cn [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China)

    2007-10-01

    The SMU.961 protein from S. mutans was crystallized and preliminary characterization of the crystals, which diffracted to 2.9 Å resolution, shows them to belong to space group C2. The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni{sup 2+}-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 Å resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 Å, β = 98.82°.

  15. Crystallization and preliminary X-ray characterization of tobacco streak virus and a proteolytically modified form of the capsid protein.

    Science.gov (United States)

    Sehnke, P C; Johnson, J E

    1993-09-01

    Isolated tobacco streak virus strain mild (TSV-M) top nucleoprotein component (TV) was crystallized by vapor diffusion with polyethylene glycol (PEG) and methyl pentanediol. The morphology of the crystal suggested a hexagonal space group, however, the crystals were disordered as analyzed by X-ray diffraction. Capsid protein from TSV (strains M and white clover) was treated with trypsin to remove 87 amino terminal residues. The modified capsid protein was purified by ion exchange chromatography and crystallized in both hexagonal and triclinic forms. Hexagonal crystals grown by vapor diffusion in PEG diffract X rays to 4.5 A. The crystals, in the space group P6(2) or its enantiomorph, possess unit cell dimensions of a = 98.3 A, c = 108.7 A and probably contain 12 dimers/unit cell. Triclinic crystals grown by vapor diffusion in ammonium sulfate diffracted X rays to 2.4 A resolution when exposed to X-ray synchrotron radiation. The crystals have unit cell dimensions of a = 60.1 A, b = 77.5 A, c = 73.9 A with alpha = 67.8 degrees, beta = 130 degrees, and gamma = 106 degrees and probably contain 4 dimers/unit cell.

  16. Cloning, crystallization and preliminary X-ray study of XC1258, a CN-hydrolase superfamily protein from Xanthomonas campestris

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Ying-Der; Chin, Ko-Hsin [Institute of Biochemistry, National Chung-Hsing University, Taichung 40227,Taiwan (China); Shr, Hui-Lin [Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei,Taiwan (China); Core Facility for Protein Crystallography, Academia Sinica, Nankang, Taipei,Taiwan (China); Gao, Fei Philip [National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310 (United States); Lyu, Ping-Chiang [Department of Life Science, National Tsing Hua University, Hsin-Chu,Taiwan (China); Wang, Andrew H.-J. [Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei,Taiwan (China); Core Facility for Protein Crystallography, Academia Sinica, Nankang, Taipei,Taiwan (China); Chou, Shan-Ho, E-mail: shchou@nchu.edu.tw [Institute of Biochemistry, National Chung-Hsing University, Taichung 40227,Taiwan (China)

    2006-10-01

    A CN-hydrolase superfamily protein from the plant pathogen X. campestris has been overexpressed in E. coli, purified and crystallized. CN-hydrolase superfamily proteins are involved in a wide variety of non-peptide carbon–nitrogen hydrolysis reactions, producing some important natural products such as auxin, biotin, precursors of antibiotics etc. These reactions all involve attack on a cyano or carbonyl carbon by a conserved novel catalytic triad Glu-Lys-Cys through a thiol acylenzyme intermediate. However, classification into the CN-hydrolase superfamily based on sequence similarity alone is not straightforward and further structural data are necessary to improve this categorization. Here, the cloning, expression, crystallization and preliminary X-ray analysis of XC1258, a CN-hydrolase superfamily protein from the plant pathogen Xanthomonas campestris (Xcc), are reported. The SeMet-substituted XC1258 crystals diffracted to a resolution of 1.73 Å. They are orthorhombic and belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 143.8, b = 154.63, c = 51.3 Å, respectively.

  17. Crystallization and preliminary X-ray diffraction studies on the bicupin YwfC from Bacillus subtilis

    Energy Technology Data Exchange (ETDEWEB)

    Rajavel, M.; Gopal, B., E-mail: bgopal@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India)

    2006-12-01

    The bicupin YwfC from B. subtilis was crystallized in two crystal forms and diffraction data were collected to 2.2 Å resolution. A central tenet of evolutionary biology is that proteins with diverse biochemical functions evolved from a single ancestral protein. A variation on this theme is that the functional repertoire of proteins in a living organism is enhanced by the evolution of single-chain multidomain polypeptides by gene-fusion or gene-duplication events. Proteins with a double-stranded β-helix (cupin) scaffold perform a diverse range of functions. Bicupins are proteins with two cupin domains. There are four bicupins in Bacillus subtilis, encoded by the genes yvrK, yoaN, yxaG and ywfC. The extensive phylogenetic information on these four proteins makes them a good model system to study the evolution of function. The proteins YvrK and YoaN are oxalate decarboxylases, whereas YxaG is a quercetin dioxygenase. In an effort to aid the functional annotation of YwfC as well as to obtain a complete structure–function data set of bicupins, it was proposed to determine the crystal structure of YwfC. The bicupin YwfC was crystallized in two crystal forms. Preliminary crystallographic studies were performed on the diamond-shaped crystals, which belonged to the tetragonal space group P422. These crystals were grown using the microbatch method at 298 K. Native X-ray diffraction data from these crystals were collected to 2.2 Å resolution on a home source. These crystals have unit-cell parameters a = b = 68.7, c = 211.5 Å. Assuming the presence of two molecules per asymmetric unit, the V{sub M} value was 2.3 Å{sup 3} Da{sup −1} and the solvent content was approximately 45%. Although the crystals appeared less frequently than the tetragonal form, YwfC also crystallizes in the monoclinic space group P2{sub 1}, with unit-cell parameters a = 46.7, b = 106.3, c = 48.7 Å, β = 92.7°.

  18. Crystallization of ornithine acetyltransferase from yeast by counter-diffusion and preliminary X-ray study

    Energy Technology Data Exchange (ETDEWEB)

    Maes, Dominique, E-mail: dominique.maes@vub.ac.be; Crabeel, Marjolaine [Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel (VUB) and Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050 Brussels (Belgium); Van de Weerdt, Cécile; Martial, Joseph [Laboratoire de Biologie Moléculaire et de Génie Génétique, Université de Liège, Allée de la Chimie 3, B-4000 Liège (Belgium); Peeters, Eveline; Charlier, Daniël [Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels (Belgium); Decanniere, Klaas; Vanhee, Celine; Wyns, Lode; Zegers, Ingrid [Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel (VUB) and Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050 Brussels (Belgium)

    2006-12-01

    A study on the crystallization of ornithine acetyltransferase from yeast, catalysing the fifth step in microbial arginine synthesis, is presented. The use of the counter-diffusion technique removes the disorder present in one dimension in crystals grown by either batch or hanging-drop techniques. A study is presented on the crystallization of ornithine acetyltransferase from yeast, which catalyzes the fifth step in microbial arginine synthesis. The use of the counter-diffusion technique removes the disorder present in one dimension in crystals grown by either the batch or hanging-drop techniques. This makes the difference between useless crystals and crystals that allow successful determination of the structure of the protein. The crystals belong to space group P4, with unit-cell parameters a = b = 66.98, c = 427.09 Å, and a data set was collected to 2.76 Å.

  19. Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

    Science.gov (United States)

    Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Sinitsyna, E. V.; Esipov, R. S.; Kuranova, I. P.

    2017-01-01

    Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus ( T. th HB27) has high thermal stability and shows maximum activity at 75°C, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P21 and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

  20. Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

    Energy Technology Data Exchange (ETDEWEB)

    Abramchik, Yu. A. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation); Muravieva, T. I.; Sinitsyna, E. V.; Esipov, R. S., E-mail: esipov@mx.ibch.ru [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)

    2017-01-15

    Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°Ð¡, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

  1. Crystallization and preliminary X-ray analysis of a phosphopentomutase from Bacillus cereus

    Energy Technology Data Exchange (ETDEWEB)

    Panosian, Timothy D.; Nannemann, David P.; Bachmann, Brian O.; Iverson, T.M. (Vanderbilt)

    2013-09-18

    Phosphopentomutases (PPMs) interconvert D-ribose 5-phosphate and {alpha}-D-ribose 1-phosphate to link glucose and nucleotide metabolism. PPM from Bacillus cereus was overexpressed in Escherichia coli, purified to homogeneity and crystallized. Bacterial PPMs are predicted to contain a di-metal reaction center, but the catalytically relevant metal has not previously been identified. Sparse-matrix crystallization screening was performed in the presence or absence of 50 mM MnCl{sub 2}. This strategy resulted in the formation of two crystal forms from two chemically distinct conditions. The crystals that formed with 50 mM MnCl{sub 2} were more easily manipulated and diffracted to higher resolution. These results suggest that even if the catalytically relevant metal is not known, the crystallization of putative metalloproteins may still benefit from supplementation of the crystallization screens with potential catalytic metals.

  2. Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca.

    Science.gov (United States)

    Singh, D D; Saikrishnan, K; Kumar, Prashant; Dauter, Z; Sekar, K; Surolia, A; Vijayan, M

    2004-11-01

    The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit. The structure has been solved using molecular replacement to a resolution of 3 A. The structure of the subunit is similar to that of jacalin-like lectins.

  3. Crystallization and preliminary X-ray analysis of Streptococcus mutans dextran glucosidase

    Energy Technology Data Exchange (ETDEWEB)

    Saburi, Wataru; Hondoh, Hironori, E-mail: hondoh@abs.agr.hokudai.ac.jp [Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589 (Japan); Unno, Hideaki [Faculty of Engineering, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521 (Japan); Okuyama, Masayuki; Mori, Haruhide [Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589 (Japan); Nakada, Toshitaka [Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577 (Japan); Matsuura, Yoshiki [Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 (Japan); Kimura, Atsuo [Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589 (Japan)

    2007-09-01

    Dextran glucosidase from S. mutans was crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.2 Å resolution. Dextran glucosidase from Streptococcus mutans is an exo-hydrolase that acts on the nonreducing terminal α-1,6-glucosidic linkage of oligosaccharides and dextran with a high degree of transglucosylation. Based on amino-acid sequence similarity, this enzyme is classified into glycoside hydrolase family 13. Recombinant dextran glucosidase was purified and crystallized by the hanging-drop vapour-diffusion technique using polyethylene glycol 6000 as a precipitant. The crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 72.72, b = 86.47, c = 104.30 Å. A native data set was collected to 2.2 Å resolution from a single crystal.

  4. Crystallization and preliminary X-ray diffraction studies on the bicupin YwfC from Bacillus subtilis

    Science.gov (United States)

    Rajavel, M.; Gopal, B.

    2006-01-01

    A central tenet of evolutionary biology is that proteins with diverse biochemical functions evolved from a single ancestral protein. A variation on this theme is that the functional repertoire of proteins in a living organism is enhanced by the evolution of single-chain multidomain polypeptides by gene-fusion or gene-duplication events. Proteins with a double-stranded β-helix (cupin) scaffold perform a diverse range of functions. Bicupins are proteins with two cupin domains. There are four bicupins in Bacillus subtilis, encoded by the genes yvrK, yoaN, yxaG and ywfC. The extensive phylogenetic information on these four proteins makes them a good model system to study the evolution of function. The proteins YvrK and YoaN are oxalate decarboxylases, whereas YxaG is a quercetin dioxygenase. In an effort to aid the functional annotation of YwfC as well as to obtain a complete structure–function data set of bicupins, it was proposed to determine the crystal structure of YwfC. The bicupin YwfC was crystallized in two crystal forms. Preliminary crystallographic studies were performed on the diamond-shaped crystals, which belonged to the tetragonal space group P422. These crystals were grown using the microbatch method at 298 K. Native X-ray diffraction data from these crystals were collected to 2.2 Å resolution on a home source. These crystals have unit-cell parameters a = b = 68.7, c = 211.5 Å. Assuming the presence of two molecules per asymmetric unit, the V M value was 2.3 Å3 Da−1 and the solvent content was approximately 45%. Although the crystals appeared less frequently than the tetragonal form, YwfC also crystallizes in the monoclinic space group P21, with unit-cell parameters a = 46.7, b = 106.3, c = 48.7 Å, β = 92.7°. PMID:17142911

  5. Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti.

    Science.gov (United States)

    Chu, Huy Nhat; Kobayashi, Jun; Yoshikane, Yu; Mikami, Bunzo; Yagi, Toshiharu

    2010-06-01

    Pyridoxal 4-dehydrogenase from Mesorhizobium loti MAFF303099 was overexpressed in Escherichia coli. The recombinant selenomethionine-substituted enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using PEG 4000 as precipitant. Crystals grew in the presence of 0.45 mM NAD(+). The crystals diffracted to 2.9 A resolution and belonged to the monoclinic space group P2(1), with unit-cell parameters a = 86.20, b = 51.11, c = 91.73 A, beta = 89.36 degrees. The calculated V(M) values suggested that the asymmetric unit contained four molecules.

  6. Crystallization and preliminary X-ray diffraction studies of Murraya koenigii trypsin inhibitor

    Science.gov (United States)

    Shee, Chandan; Singh, Tej P.; Kumar, Pravindra; Sharma, Ashwani K.

    2007-01-01

    A Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. The crystals belong to the tetragonal space group P43212, with unit-cell parameters a = b = 75.8, c = 150.9 Å. The crystals contain two molecules in the asymmetric unit with a V M value of 2.5 Å3 Da−1. Diffraction was observed to 2.65 Å resolution and a complete data set was collected to 2.9 Å resolution. PMID:17401205

  7. Crystallization and preliminary X-ray diffraction analysis of the hyperthermophilic Sulfolobus solfataricus phosphotriesterase

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael [Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Dupuy, Jérôme [Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble (France); Merone, Luigia [Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli (Italy); Lecomte, Claude [Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Rossi, Mosè [Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli (Italy); Masson, Patrick [Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France); Manco, Giuseppe [Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli (Italy); Chabriere, Eric, E-mail: eric.chabriere@lcm3b.uhp-nancy.fr [Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France)

    2007-07-01

    A phosphotriesterase (PTE) from the hyperthermophilic archaeon S. solfataricus has been crystallized. Combined with biochemical and bioengineering studies, it is expected that the structure of this protein will provide insight into the natural function of the PTE family and provide important data for achieving an efficient organophosphate biodecontaminant. Organophosphates constitute the largest class of insecticides used worldwide and some of them are potent nerve agents. Consequently, organophosphate-degrading enzymes are of paramount interest as they could be used as bioscavengers and biodecontaminants. Phosphotriesterases (PTEs) are capable of hydrolyzing these toxic compounds with high efficiency. A distant and hyperthermophilic representative of the PTE family was cloned from the archeon Sulfolobus solfataricus MT4, overexpressed in Escherichia coli and crystallized; the crystals diffracted to 2.54 Å resolution. Owing to its exceptional thermostability, this PTE may be an excellent candidate for obtaining an efficient organophosphate biodecontaminant. Here, the crystallization conditions and data collection for the hyperthermophilic S. solfataricus PTE are reported.

  8. Crystallization and preliminary X-ray diffraction studies of Murraya koenigii trypsin inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Shee, Chandan [Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667 (India); Singh, Tej P. [Department of Biophysics, All India Institute of Medical Sciences, New Delhi 100 029 (India); Kumar, Pravindra, E-mail: kumarfbs@iitr.ernet.in; Sharma, Ashwani K., E-mail: kumarfbs@iitr.ernet.in [Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667 (India)

    2007-04-01

    A Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. A Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. The crystals belong to the tetragonal space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 75.8, c = 150.9 Å. The crystals contain two molecules in the asymmetric unit with a V{sub M} value of 2.5 Å{sup 3} Da{sup −1}. Diffraction was observed to 2.65 Å resolution and a complete data set was collected to 2.9 Å resolution.

  9. Crystallization and preliminary X-ray characterization of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis

    Energy Technology Data Exchange (ETDEWEB)

    Nakajima, Yoshitaka; Ito, Kiyoshi, E-mail: k-ito@net.nagasaki-u.ac.jp; Xu, Yue; Yamada, Nozomi; Onohara, Yuko; Ito, Takashi; Yoshimoto, Tadashi [Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521 (Japan)

    2005-12-01

    P. gingivalis prolyl tripeptidyl aminopeptidase has been crystallized by the vapour-diffusion method. Diffraction data have been collected and processed to 2.1 Å resolution. A recombinant form of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis has been crystallized by the hanging-drop vapour-diffusion method using potassium sodium tartrate as a precipitating agent. The crystals belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 149.4, c = 159.7 Å. The crystals are most likely to contain one subunit of a dimer in the asymmetric unit, with a V{sub M} value of 3.14 Å{sup 3} Da{sup −1}. Diffraction data were collected to 2.1 Å resolution using synchrotron radiation at the BL5 station of the Photon Factory.

  10. Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

    Science.gov (United States)

    Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

    2016-11-01

    Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P1211 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

  11. Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

    Energy Technology Data Exchange (ETDEWEB)

    Abramchik, Yu. A. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation); Muravieva, T. I.; Esipov, R. S., E-mail: espiov@mx.ibch.ru [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation)

    2016-11-15

    Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12{sub 1}1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

  12. Purification, crystallization and preliminary X-ray characterization of the human GTP fucose pyrophosphorylase

    Energy Technology Data Exchange (ETDEWEB)

    Quirk, Stephen; Seley-Radtke, Katherine L., E-mail: kseley@umbc.edu [Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Chemistry 405C, Baltimore, MD 21250 (United States)

    2006-04-01

    The human GTP fucose pyrophosphohydrolase protein has been crystallized via the hanging-drop technique over a reservoir of polyethylene glycol (MW 8000) and ethylene glycol. The orthorhombic crystals diffract to 2.8 Å resolution. The human nucleotide-sugar metabolizing enzyme GTP fucose pyrophosphorylase (GFPP) has been purified to homogeneity by an affinity chromatographic procedure that utilizes a novel nucleoside analog. This new purification regime results in a protein preparation that produces significantly better crystals than traditional purification methods. The purified 66.6 kDa monomeric protein has been crystallized via hanging-drop vapor diffusion at 293 K. Crystals of the native enzyme diffract to 2.8 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}. There is a single GFPP monomer in the asymmetric unit, giving a Matthews coefficient of 2.38 Å{sup 3} Da{sup −1} and a solvent content of 48.2%. A complete native data set has been collected as a first step in determining the three-dimensional structure of this enzyme.

  13. Crystallization and preliminary X-ray diffraction analysis of a lectin from Canavalia maritima seeds

    Energy Technology Data Exchange (ETDEWEB)

    Almeida Gadelha, Carlos Alberto de [BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Caixa Postal 6043, CEP 60455-970 (Brazil); Moreno, Frederico Bruno Mendes Batista [Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil); Santi-Gadelha, Tatiane; Cajazeiras, João Batista; Rocha, Bruno Anderson M. da [BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Caixa Postal 6043, CEP 60455-970 (Brazil); Rustiguel, Joane Kathelen Rodrigues [Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil); Freitas, Beatriz Tupinamba [BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Caixa Postal 6043, CEP 60455-970 (Brazil); Grupo de Química Biológica, Departamento de Ciências Biológicas, Universidade Regional do Cariri, Crato, CE 63195-000 (Brazil); Canduri, Fernanda [Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil); Delatorre, Plínio [BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Caixa Postal 6043, CEP 60455-970 (Brazil); Grupo de Química Biológica, Departamento de Ciências Biológicas, Universidade Regional do Cariri, Crato, CE 63195-000 (Brazil); Azevedo, Walter Filgueira Jr de, E-mail: walterfa@df.ibilce.unesp.br [Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil); Cavada, Benildo S., E-mail: walterfa@df.ibilce.unesp.br [BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Caixa Postal 6043, CEP 60455-970 (Brazil)

    2005-01-01

    A lectin from C. maritima was crystallized using the vapour-diffusion method and crystals diffracted to 2.1 Å resolution. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%, refinement is in progress. A lectin from Canavalia maritima seeds (ConM) was purified and submitted to crystallization experiments. The best crystals were obtained using the vapour-diffusion method at a constant temperature of 293 K and grew in 7 d. A complete structural data set was collected to 2.1 Å resolution using a synchrotron-radiation source. The ConM crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 67.15, b = 70.90, c = 97.37 Å. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%. Crystallographic refinement is under way.

  14. Crystallization and preliminary X-ray diffraction studies of a catechol-O-methyltransferase/inhibitor complex

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, M. L. [Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras (Portugal); Bonifácio, M. J.; Soares-da-Silva, P. [Department of Research and Development, BIAL, 4785 S. Mamede do Coronado (Portugal); Carrondo, M. A.; Archer, M., E-mail: archer@itqb.unl.pt [Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras (Portugal)

    2005-01-01

    Catechol-O-methyltransferase has been co-crystallized with a novel inhibitor, which has potential therapeutic application in the Parkinson’s disease therapy. Inhibitors of the enzyme catechol-O-methyltransferase (COMT) are used as co-adjuvants in the therapy of Parkinson’s disease. A recombinant form of the soluble cytosolic COMT from rat has been co-crystallized with a new potent inhibitor, BIA 8-176 [(3,4-dihydroxy-2-nitrophenyl)phenylmethanone], by the vapour-diffusion method using PEG 6K as precipitant. Crystals diffract to 1.6 Å resolution on a synchrotron-radiation source and belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 52.77, b = 79.63, c = 61.54 Å, β = 91.14°.

  15. Expression, purification, crystallization and preliminary X-ray studies of Lactobacillus jensenii enolase

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Paul T.; Raghunathan, Kannan; Spurbeck, Rachel R.; Arvidson, Cindy G.; Arvidson, Dennis N. (MSU)

    2010-09-02

    Recombinant Lactobacillus jensenii enolase fused to a C-terminal noncleavable His tag was expressed in Escherichia coli, purified and crystallized by sitting-drop vapor diffusion. A complete data set was collected to 3.25 {angstrom} resolution. The crystals belonged to space group I4, with unit-cell parameters a = b = 145.31, c = 99.79 {angstrom}. There were two protein subunits in the asymmetric unit, which gave a Matthews coefficient V{sub M} of 2.8 {angstrom}{sup 3} Da{sup -1}, corresponding to 55.2% solvent content.

  16. Crystallization and preliminary X-ray diffraction studies of the pneumococcal teichoic acid phosphorylcholine esterase Pce

    Energy Technology Data Exchange (ETDEWEB)

    Lagartera, Laura; González, Ana; Stelter, Meike; García, Pedro; Kahn, Richard; Menéndez, Margarita; Hermoso, Juan A., E-mail: xjuan@iqfr.csic.es

    2005-02-01

    The modular choline-binding protein Pce, the phosphorylcholine esterase from S. pneumoniae, has been crystallized by the hanging-drop vapour-diffusion method. A SAD data set from a derivative with a gadolinium complex has been collected to 2.7 Å resolution.

  17. Crystallization and preliminary X-ray studies of ferredoxin-NAD(P)+ reductase from Chlorobium tepidum.

    Science.gov (United States)

    Muraki, Norifumi; Seo, Daisuke; Shiba, Tomoo; Sakurai, Takeshi; Kurisu, Genji

    2008-03-01

    Ferredoxin-NAD(P)(+) reductase (FNR) is a key enzyme that catalyzes the photoreduction of NAD(P)(+) to generate NAD(P)H during the final step of the photosynthetic electron-transport chain. FNR from the green sulfur bacterium Chlorobium tepidum is a homodimeric enzyme with a molecular weight of 90 kDa; it shares a high level of amino-acid sequence identity to thioredoxin reductase rather than to conventional plant-type FNRs. In order to understand the structural basis of the ferredoxin-dependency of this unique photosynthetic FNR, C. tepidum FNR has been heterologously expressed, purified and crystallized in two forms. Form I crystals belong to space group C222(1) and contain one dimer in the asymmetric unit, while form II crystals belong to space group P4(1)22 or P4(3)22. Diffraction data were collected from a form I crystal to 2.4 A resolution on the synchrotron-radiation beamline NW12 at the Photon Factory.

  18. Crystallization and preliminary X-ray diffraction analysis of Nsp15 from SARS coronavirus

    Energy Technology Data Exchange (ETDEWEB)

    Ricagno, Stéfano; Coutard, Bruno; Grisel, Sacha; Brémond, Nicolas; Dalle, Karen; Tocque, Fabienne; Campanacci, Valérie; Lichière, Julie; Lantez, Violaine; Debarnot, Claire; Cambillau, Christian; Canard, Bruno; Egloff, Marie-Pierre, E-mail: marie-pierre.egloff@afmb.univ-mrs.fr [Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9 (France)

    2006-04-01

    Crystals of Nsp15 from the aetiological agent of SARS have been grown at room temperature. Crystals have cubic symmetry and diffract to a maximum resolution of 2.7 Å. The non-structural protein Nsp15 from the aetiological agent of SARS (severe acute respiratory syndrome) has recently been characterized as a uridine-specific endoribonuclease. This enzyme plays an essential role in viral replication and transcription since a mutation in the related H229E human coronavirus nsp15 gene can abolish viral RNA synthesis. SARS full-length Nsp15 (346 amino acids) has been cloned and expressed in Escherichia coli with an N-terminal hexahistidine tag and has been purified to homogeneity. The protein was subsequently crystallized using PEG 8000 or 10 000 as precipitants. Small cubic crystals of the apoenzyme were obtained from 100 nl nanodrops. They belong to space group P4{sub 1}32 or P4{sub 3}32, with unit-cell parameters a = b = c = 166.8 Å. Diffraction data were collected to a maximum resolution of 2.7 Å.

  19. Purification, crystallization and preliminary X-ray diffraction analysis of the human mismatch repair protein MutSβ

    Science.gov (United States)

    Tseng, Quincy; Orans, Jillian; Hast, Michael A.; Iyer, Ravi R.; Changela, Anita; Modrich, Paul L.; Beese, Lorena S.

    2011-01-01

    MutSβ is a eukaryotic mismatch repair protein that preferentially targets extrahelical unpaired nucleotides and shares partial functional redundancy with MutSα (MSH2–MSH6). Although mismatch recognition by MutSα has been shown to involve a conserved Phe-X-Glu motif, little is known about the lesion-binding mechanism of MutSβ. Combined MSH3/MSH6 deficiency triggers a strong predisposition to cancer in mice and defects in msh2 and msh6 account for roughly half of hereditary nonpolyposis colorectal cancer mutations. These three MutS homologs are also believed to play a role in trinucleotide repeat instability, which is a hallmark of many neurodegenerative disorders. The baculovirus overexpression and purification of recombinant human MutSβ and three truncation mutants are presented here. Binding assays with heteroduplex DNA were carried out for biochemical characterization. Crystallization and preliminary X-ray diffraction analysis of the protein bound to a heteroduplex DNA substrate are also reported. PMID:21821902

  20. Purification, crystallization and preliminary X-ray diffraction analysis of the human mismatch repair protein MutS[beta

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, Quincy; Orans, Jillian; Hast, Michael A.; Iyer, Ravi R.; Changela, Anita; Modrich, Paul L.; Beese, Lorena S. (Duke)

    2012-03-16

    MutS{beta} is a eukaryotic mismatch repair protein that preferentially targets extrahelical unpaired nucleotides and shares partial functional redundancy with MutS{alpha} (MSH2-MSH6). Although mismatch recognition by MutS{alpha} has been shown to involve a conserved Phe-X-Glu motif, little is known about the lesion-binding mechanism of MutS{beta}. Combined MSH3/MSH6 deficiency triggers a strong predisposition to cancer in mice and defects in msh2 and msh6 account for roughly half of hereditary nonpolyposis colorectal cancer mutations. These three MutS homologs are also believed to play a role in trinucleotide repeat instability, which is a hallmark of many neurodegenerative disorders. The baculovirus overexpression and purification of recombinant human MutS{beta} and three truncation mutants are presented here. Binding assays with heteroduplex DNA were carried out for biochemical characterization. Crystallization and preliminary X-ray diffraction analysis of the protein bound to a heteroduplex DNA substrate are also reported.

  1. Purification, crystallization and preliminary X-ray diffraction of human S100A15

    Energy Technology Data Exchange (ETDEWEB)

    Boeshans, Karen M. [X-ray Crystallography Facility, NIAMS, National Institutes of Health, Bethesda, MD 20892 (United States); Wolf, Ronald; Voscopoulos, Christopher [Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States); Gillette, William; Esposito, Dominic [Protein Expression Laboratory, Research Technology Program, National Cancer Institute, SAIC-Frederick Inc., Frederick, MD 21702 (United States); Mueser, Timothy C. [Department of Chemistry, University of Toledo, Toledo, OH 43606 (United States); Yuspa, Stuart H. [Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States); Ahvazi, Bijan, E-mail: ahvazib@mail.nih.gov [X-ray Crystallography Facility, NIAMS, National Institutes of Health, Bethesda, MD 20892 (United States)

    2006-05-01

    S100 proteins are differentially expressed during epithelial cell maturation, tumorigenesis and inflammation. The novel human S100A15 protein has been cloned, expressed, purified and crystallized in two crystal forms, a triclinic and a monoclinic form, which diffract to 1.7 and 2.0 Å, respectively. Human S100A15 is a novel member of the S100 family of EF-hand calcium-binding proteins and was recently identified in psoriasis, where it is significantly upregulated in lesional skin. The protein is implicated as an effector in calcium-mediated signal transduction pathways. Although its biological function is unclear, the association of the 11.2 kDa S100A15 with psoriasis suggests that it contributes to the pathogenesis of the disease and could provide a molecular target for therapy. To provide insight into the function of S100A15, the protein was crystallized to visualize its structure and to further the understanding of how the many similar calcium-binding mediator proteins in the cell distinguish their cognate target molecules. The S100A15 protein has been cloned, expressed and purified to homogeneity and produced two crystal forms. Crystals of form I are triclinic, with unit-cell parameters a = 33.5, b = 44.3, c = 44.8 Å, α = 71.2, β = 68.1, γ = 67.8° and an estimated two molecules in the asymmetric unit, and diffract to 1.7 Å resolution. Crystals of form II are monoclinic, with unit-cell parameters a = 82.1, b = 33.6, c = 52.2 Å, β = 128.2° and an estimated one molecule in the asymmetric unit, and diffract to 2.0 Å resolution. This structural analysis of the human S100A15 will further aid in the phylogenic comparison between the other members of the S100 protein family, especially the highly homologous paralog S100A7.

  2. Crystallization and preliminary X-ray crystallographic analysis of MacA from Actinobacillus actinomycetemcomitans

    Energy Technology Data Exchange (ETDEWEB)

    Piao, Shunfu; Xu, Yongbin; Ha, Nam-Chul, E-mail: hnc@pusan.ac.kr [College of Pharmacy and Research Institute for Drug Development, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735 (Korea, Republic of)

    2008-05-01

    A periplasmic membrane-fusion protein MacA from Actinobacillus actinomycetemcomitans, an essential component of the multidrug efflux pump in Gram-negative bacteria, was crystallized. Periplasmic membrane-fusion proteins (MFPs) are an essential component of the multidrug efflux pump in Gram-negative bacteria. They play a crucial role in bridging the outer membrane porin TolC and two distinct types of inner membrane transporters. The MFP MacA bridges the inner membrane ABC-type multidrug transporter MacB and the outer membrane porin TolC. MacA from the pathogenic bacterium Actinobacillus actinomycetemcomitans was expressed in Escherichia coli B834 (DE3) and the recombinant protein was purified using Ni–NTA affinity, Q anion-exchange and gel-filtration chromatography. The purified MacA protein was crystallized using the vapour-diffusion method. A MAD diffraction data set was collected to a resolution of 3.0 Å at 100 K. The crystal belongs to space group P622, with unit-cell parameters a = b = 109.2, c = 255.4 Å, α = β = 90, γ = 120°, and contains one molecule in the asymmetric unit.

  3. Crystallization and preliminary X-ray diffraction studies of the glutaminyl cyclase from Carica papaya latex

    Energy Technology Data Exchange (ETDEWEB)

    Azarkan, Mohamed [Laboratoire de Chimie Générale I, Faculté de Médecine-ULB CP609, 808 Route de Lennik, B-1070 Brussels (Belgium); Clantin, Bernard; Bompard, Coralie [CNRS-UMR 8525, Institut de Biologie de Lille, BP 477, 1 Rue du Professeur Calmette, F-59021 Lille (France); Belrhali, Hassan [EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP 181, F-38042 Grenoble CEDEX 9 (France); Baeyens-Volant, Danielle [Laboratoire de Chimie Générale I, Faculté de Médecine-ULB CP609, 808 Route de Lennik, B-1070 Brussels (Belgium); Looze, Yvan [Laboratoire de Chimie Générale, Institut de Pharmacie-ULB CP206/04, Boulevard du Triomphe, B-1050 Brussels (Belgium); Villeret, Vincent, E-mail: vincent.villeret@ibl.fr [CNRS-UMR 8525, Institut de Biologie de Lille, BP 477, 1 Rue du Professeur Calmette, F-59021 Lille (France); Wintjens, René, E-mail: vincent.villeret@ibl.fr [Laboratoire de Chimie Générale, Institut de Pharmacie-ULB CP206/04, Boulevard du Triomphe, B-1050 Brussels (Belgium); Laboratoire de Chimie Générale I, Faculté de Médecine-ULB CP609, 808 Route de Lennik, B-1070 Brussels (Belgium)

    2005-01-01

    The glutaminyl cyclase isolated from C. papaya latex has been crystallized using the hanging-drop method. Diffraction data have been collected at ESRF beamline BM14 and processed to 1.7 Å resolution. In living systems, the intramolecular cyclization of N-terminal glutamine residues is accomplished by glutaminyl cyclase enzymes (EC 2.3.2.5). While in mammals these enzymes are involved in the synthesis of hormonal and neurotransmitter peptides, the physiological role played by the corresponding plant enzymes still remains to be unravelled. Papaya glutaminyl cyclase (PQC), a 33 kDa enzyme found in the latex of the tropical tree Carica papaya, displays an exceptional resistance to chemical and thermal denaturation as well as to proteolysis. In order to elucidate its enzymatic mechanism and to gain insights into the structural determinants underlying its remarkable stability, PQC was isolated from papaya latex, purified and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 62.82, b = 81.23, c = 108.17 Å and two molecules per asymmetric unit. Diffraction data have been collected at ESRF beamline BM14 and processed to a resolution of 1.7 Å.

  4. Purification, crystallization and preliminary X-ray analysis of phycocyanin and phycoerythrin from Porphyra yezoensis Ueda.

    Science.gov (United States)

    Cai, Chuner; Wu, Lian; Li, Chunxia; He, Peimin; Li, Jie; Zhou, Jiahai

    2011-05-01

    Porphyra yezoensis is one of the most important and widely cultured seaweeds in China. Phycobiliproteins exhibit excellent spectroscopic properties and play versatile roles in the biomedical, food, cosmetics and chemical synthetic dye industries. Here, the purification and crystallization of phycoerythrin and phycocyanin, two phycobiliproteins extracted from P. yezoensis, are described. Using a novel protocol including co-precipitation with ammonium sulfate and hydroxyapatite column chromatography, both phycobiliproteins were produced on a large scale with improved quality and yield compared with those previously reported. Native PAGE analysis indicated that phycoerythrin and phycocyanin exist as (αβ)(3) heterohexamers in solution. The crystals of phycoerythrin diffracted to 2.07 Å resolution and belonged to space group R3. The unit-cell parameters referred to hexagonal axes are a = b = 187.7, c = 59.7 Å, with nine (αβ)(2) heterotetramers per unit cell. The crystals of phycocyanin diffracted to 2.70 Å resolution in space group P2(1). Matthews coefficient analysis shows that 10-19 (αβ) heterodimers of phycocyanin in the asymmetric unit would be reasonable. A self-rotation function calculation clarified this ambiguity and indicated that 12 (αβ) heterodimers of phycocyanin are assembled in the asymmetric unit.

  5. Purification, crystallization and preliminary x-ray crystallographic studies of RAIDD Death-Domain (DD).

    Science.gov (United States)

    Jang, Tae-ho; Park, Hyun Ho

    2009-06-03

    Caspase-2 activation by formation of PIDDosome is critical for genotoxic stress induced apoptosis. PIDDosome is composed of three proteins, RAIDD, PIDD, and Caspase-2. RAIDD is an adaptor protein containing an N-terminal Caspase-Recruiting-Domain (CARD) and a C-terminal Death-Domain (DD). Its interactions with Caspase-2 and PIDD through CARD and DD respectively and formation of PIDDosome are important for the activation of Caspase-2. RAIDD DD cloned into pET26b vector was expressed in E. coli cells and purified by nickel affinity chromatography and gel filtration. Although it has been known that the most DDs are not soluble in physiological condition, RAIDD DD was soluble and interacts tightly with PIDD DD in physiological condition. The purified RAIDD DD alone has been crystallized. Crystals are trigonal and belong to space group P3(1)21 (or its enantiomorph P3(2)21) with unit-cell parameters a = 56.3, b = 56.3, c = 64.9 A and gamma = 120 degrees . The crystals were obtained at room temperature and diffracted to 2.0 A resolution.

  6. Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15

    Energy Technology Data Exchange (ETDEWEB)

    Ochiai, Akihito [Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Yamasaki, Masayuki; Mikami, Bunzo [Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Hashimoto, Wataru; Murata, Kousaku, E-mail: kmurata@kais.kyoto-u.ac.jp [Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2006-05-01

    The crystallization and preliminary X-ray characterization of a family PL-15 exotype alginate lyase are presented. Almost all alginate lyases depolymerize alginate in an endolytical fashion via a β-elimination reaction. The alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, consisting of 776 amino-acid residues, is a novel exotype alginate lyase classified into polysaccharide lyase family 15. The enzyme was crystallized at 293 K by sitting-drop vapour diffusion with polyethylene glycol 4000 as a precipitant. Preliminary X-ray analysis showed that the Atu3025 crystal belonged to space group P2{sub 1} and diffracted to 2.8 Å resolution, with unit-cell parameters a = 107.7, b = 108.3, c = 149.5 Å, β = 91.5°.

  7. Overexpression, crystallization and preliminary X-ray crystallographic analysis of a putative xylose isomerase from Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Cho, Jea-Won; Han, Byeong-Gu; Park, Sang Youn; Kim, Seung Jun; Kim, Myoung-Dong; Lee, Byung Il

    2013-10-01

    Bacteroides thetaiotaomicron BT0793, a putative xylose isomerase, was overexpressed in Escherichia coli, purified and crystallized using polyethylene glycol monomethyl ether 550 as the precipitant. X-ray diffraction data were collected to 2.10 Å resolution at 100 K using synchrotron X-rays. The crystal was found to belong to space group P1, with unit-cell parameters a=96.3, b=101.7, c=108.3 Å, α=82.8, β=68.2, γ=83.0°. The asymmetric unit contained eight subunits of xylose isomerase with a crystal volume per protein weight (VM) of 2.38 Å3 Da(-1) and a solvent content of 48.3%.

  8. Crystallization and preliminary X-ray data analysis of beta-alanine synthase from Drosophila melanogaster.

    Science.gov (United States)

    Lundgren, Stina; Andersen, Birgit; Piskur, Jure; Dobritzsch, Doreen

    2007-10-01

    Beta-alanine synthase catalyzes the last step in the reductive degradation pathway for uracil and thymine, which represents the main clearance route for the widely used anticancer drug 5-fluorouracil. Crystals of the recombinant enzyme from Drosophila melanogaster, which is closely related to the human enzyme, were obtained by the hanging-drop vapour-diffusion method. They diffracted to 3.3 A at a synchrotron-radiation source, belong to space group C2 (unit-cell parameters a = 278.9, b = 95.0, c = 199.3 A, beta = 125.8 degrees) and contain 8-10 molecules per asymmetric unit.

  9. Expression, purification, crystallization and preliminary X-ray diffraction analysis of acylpeptide hydrolase from Deinococcus radiodurans.

    Science.gov (United States)

    Are, Venkata Narayana; Ghosh, Biplab; Kumar, Ashwani; Yadav, Pooja; Bhatnagar, Deepak; Jamdar, Sahayog N; Makde, Ravindra D

    2014-09-01

    Acylpeptide hydrolase (APH; EC 3.4.19.1), which belongs to the S9 family of serine peptidases (MEROPS), catalyzes the removal of an N-acylated amino acid from a blocked peptide. The role of this enzyme in mammalian cells has been suggested to be in the clearance of oxidatively damaged proteins as well as in the degradation of the β-amyloid peptides implicated in Alzheimer's disease. Detailed structural information for the enzyme has been reported from two thermophilic archaea; both of the archaeal APHs share a similar monomeric structure. However, the mechanisms of substrate selectivity and active-site accessibility are totally different and are determined by inter-domain flexibility or the oligomeric structure. An APH homologue from a bacterium, Deinococcus radiodurans (APHdr), has been crystallized using microbatch-under-oil employing the random microseed matrix screening method. The protein crystallized in space group P21, with unit-cell parameters a = 77.6, b = 189.6, c = 120.4 Å, β = 108.4°. A Matthews coefficient of 2.89 Å(3) Da(-1) corresponds to four monomers, each with a molecular mass of ∼73 kDa, in the asymmetric unit. The APHdr structure will reveal the mechanisms of substrate selectivity and active-site accessibility in the bacterial enzyme. It will also be helpful in elucidating the functional role of this enzyme in D. radiodurans.

  10. Purification, crystallization and preliminary X-ray diffraction studies of the archaeal virus resolvase SIRV2

    Energy Technology Data Exchange (ETDEWEB)

    Ennifar, Eric [European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg (Germany); UPR9002 CNRS, associated with the Université Louis Pasteur, 15 Rue René Descartes, F-67084 Strasbourg (France); Basquin, Jerôme [European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg (Germany); Birkenbihl, Rainer [MPI für Züchtungsforschung, Carl-von-Linné-Weg 10, 50829 Köln (Germany); Suck, Dietrich, E-mail: suck@embl.de [European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg (Germany)

    2005-05-01

    The Holliday junction resolvase of the archaeal virus SIRV2 infecting the archaeon Sulfolobus islandicus has been crystallized and a full data set has been collected at 3.4 Å resolution. Analysis of the self-rotation function suggests the presence of two dimers in the asymmetric unit with a solvent content of 77%. The Holliday junction (or four-way junction) is the universal DNA intermediate whose interaction with resolving proteins is one of the major events in the recombinational process. These proteins, called DNA junction-resolving enzymes or resolvases, bind to the junction and catalyse DNA cleavage, promoting the release of two DNA duplexes. SIRV2 Hjc, a viral resolvase infecting a thermophylic archaeon, has been cloned, expressed and purified. Crystals have been obtained in space group C2, with unit-cell parameters a = 147.8, b = 99.9, c = 87.6, β = 109.46°, and a full data set has been collected at 3.4 Å resolution. The self-rotation function indicates the presence of two dimers in the asymmetric unit and a high solvent content (77%). Molecular-replacement trials using known similar resolvase structures have so far been unsuccessful, indicating possible significant structural rearrangements.

  11. Crystallization and preliminary X-ray diffraction of the Munc18c–syntaxin4{sub 1–29} complex

    Energy Technology Data Exchange (ETDEWEB)

    Latham, Catherine F.; Hu, Shu-Hong; Gee, Christine L.; Armishaw, Chris J.; Alewood, Paul F. [Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072 (Australia); James, David E. [Garvan Institute of Medical Research, Darlinghurst, NSW 2010 (Australia); Martin, Jennifer L., E-mail: j.martin@imb.uq.edu.au [Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072 (Australia)

    2007-06-01

    Cocrystallization with a peptide, free-interface diffusion crystal chips and crystal dehydration were important in the production of diffraction-quality crystals of the Munc18c protein that helps to regulate membrane fusion. The production of diffraction-quality crystals of Munc18c, a protein involved in regulating vesicular exocytosis in mammals, is reported. The diffraction resolution of Munc18c crystals was optimized by (i) cocrystallizing with a peptide fragment of the Munc18c functional binding partner syntaxin4, (ii) using nanolitre free-interface diffusion crystallization-screening chips and microlitre hanging-drop vapour diffusion and (iii) applying a post-crystallization dehydration treatment. Crystals belonging to the cubic space group P2{sub 1}3, with unit-cell parameters a = b = c = 170.8 Å, α = β = γ = 90°, were generated that diffract to 3.7 Å resolution on a laboratory X-ray source.

  12. Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Kan [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Suzuki, Takehiro; Dohmae, Naoshi [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Ishitani, Ryuichiro [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)

    2014-08-27

    E. coli YfcM was expressed, purified and crystallized. Crystals of YfcM were obtained by the in situ proteolysis crystallization method. Using these crystals, an X-ray diffraction data set was collected at 1.45 Å resolution. Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (V{sub M}) of the crystal was 1.91 Å{sup 3} Da{sup −1}, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.

  13. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of a cyclophilin A-like protein from Piriformospora indica.

    Science.gov (United States)

    Bhatt, Harshesh; Trivedi, Dipesh Kumar; Pal, Ravi Kant; Johri, Atul Kumar; Tuteja, Narendra; Bhavesh, Neel Sarovar

    2012-06-01

    Cyclophilins are widely distributed both in eukaryotes and prokaryotes and have a primary role as peptidyl-prolyl cis-trans isomerases (PPIases). This study focuses on the cloning, expression, purification and crystallization of a salinity-stress-induced cyclophilin A (CypA) homologue from the symbiotic fungus Piriformospora indica. Crystallization experiments in the presence of 56 mM sodium phosphate monobasic monohydrate, 1.34 M potassium phosphate dibasic pH 8.2 yielded crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 121.15, b = 144.12, c = 110.63 Å. The crystals diffracted to a resolution limit of 2.0 Å. Analysis of the diffraction data indicated the presence of three molecules of the protein per asymmetric unit (V(M) = 4.48 Å(3) Da(-1), 72.6% solvent content).

  14. Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

    Science.gov (United States)

    Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Popov, V. O.

    2017-11-01

    The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

  15. Purification, crystallization and preliminary X-ray diffraction studies of UDP-N-acetylglucosamine pyrophosphorylase from Candida albicans

    Energy Technology Data Exchange (ETDEWEB)

    Maruyama, Daisuke; Nishitani, Yuichi; Nonaka, Tsuyoshi; Kita, Akiko [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); Fukami, Takaaki A.; Mio, Toshiyuki; Yamada-Okabe, Hisafumi [Kamakura Research Laboratory, Chugai Pharmaceutical Co. Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530 (Japan); Yamada-Okabe, Toshiko [Department of Hygiene, School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama 236-0004 (Japan); Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp [Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayocho, Sayo-gun, Hyogo 679-5148 (Japan)

    2006-12-01

    UDP-N-acetylglucosamine pyrophosphorylase was purified and crystallized and X-ray diffraction data were collected to 2.3 Å resolution. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is an essential enzyme in the synthesis of UDP-N-acetylglucosamine. UAP from Candida albicans was purified and crystallized by the sitting-drop vapour-diffusion method. The crystals of the substrate and product complexes both diffract X-rays to beyond 2.3 Å resolution using synchrotron radiation. The crystals of the substrate complex belong to the triclinic space group P1, with unit-cell parameters a = 47.77, b = 62.89, c = 90.60 Å, α = 90.01, β = 97.72, γ = 92.88°, whereas those of the product complex belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.95, b = 90.87, c = 94.88 Å.

  16. Crystallization and preliminary X-ray diffraction analysis of the haem-binding protein HemS from Yersinia enterocolitica

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Sabine; Paoli, Massimo, E-mail: max.paoli@nottingham.ac.uk [School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

    2005-08-01

    The haem binding protein HemS from Y. enterocolitica has been crystallized in complex with its ligand. The crystals diffracted X-rays to 2.6 Å in-house. Bacteria have evolved strategies to acquire iron from their environment. Pathogenic microbes rely on specialized proteins to ‘steal’ haem from their host and use it as an iron source. HemS is the ultimate recipient of a molecular-relay system for haem uptake in Gram-negative species, functioning as the cytosolic carrier of haem. Soluble expression and high-quality diffraction crystals were obtained for HemS from Yersinia enterocolitica. Crystals belong to the orthorhombic space group I222, with unit-cell parameters a = 74.86, b = 77.45, c = 114.09 Å, and diffract X-rays to 2.6 Å spacing in-house. Determination of the structure of the haem–HemS complex will reveal the molecular basis of haem binding.

  17. Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus

    Energy Technology Data Exchange (ETDEWEB)

    Carr, Stephen B., E-mail: bmbsbc@bmb.leeds.ac.uk [Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (United Kingdom); Makris, George [Omega Mediation Hellas Ltd, Clinical and Pharma Consulting, 11525 N. Psychiko, Athens (Greece); Phillips, Simon E. V.; Thomas, Christopher D. [Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2006-11-01

    The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed. DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-ray analysis revealed that GrlA56 crystals belong to space group P2{sub 1}, diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism.

  18. Crystallization and preliminary X-ray diffraction study of an active-site mutant of pro-Tk-subtilisin from a hyperthermophilic archaeon

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Shun-ichi; Saito, Kenji; Chon, Hyongi [Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Matsumura, Hiroyoshi [Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); CREST (Sosho Project), JST, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Koga, Yuichi [Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Takano, Kazufumi [Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); CREST (Sosho Project), JST, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kanaya, Shigenori, E-mail: kanaya@mls.eng.osaka-u.ac.jp [Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2006-09-01

    Crystallization of and preliminary crystallographic studies on an active-site mutant of pro-Tk-subtilisin from the hyperthermophilic archaeon T. kodakaraensis were performed. Crystallization of and preliminary crystallographic studies on an active-site mutant of pro-Tk-subtilisin from the hyperthermophilic archaeon Thermococcus kodakaraensis were performed. The crystal was grown at 277 K by the sitting-drop vapour-diffusion method. Native X-ray diffraction data were collected to 2.3 Å resolution using synchrotron radiation from station BL41XU at SPring-8. The crystal belongs to the orthorhombic space group I222, with unit-cell parameters a = 92.69, b = 121.78, c = 77.53 Å. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V{sub M} was calculated to be 2.6 Å{sup 3} Da{sup −1} and the solvent content was 53.1%.

  19. Purification, crystallization and preliminary X-ray analysis of Enterococcus faecium aminoglycoside-2′′-phosphotransferase-Ib [APH(2′′)-Ib

    Energy Technology Data Exchange (ETDEWEB)

    Walanj, Rupa; Young, Paul; Baker, Heather M.; Baker, Edward N.; Metcalf, Peter [Laboratory of Structural Biology, School of Biological Sciences, University of Auckland, Auckland (New Zealand); Chow, Joseph W.; Lerner, Stephen [Division of Infectious Diseases, Wayne State University School of Medicine and VA Medical Center, Detroit, Michigan 48201 (United States); Vakulenko, Sergei [Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 (United States); Smith, Clyde A., E-mail: csmith@slac.stanford.edu [Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025 (United States); Laboratory of Structural Biology, School of Biological Sciences, University of Auckland, Auckland (New Zealand)

    2005-04-01

    APH(2′′)-Ib is an enzyme responsible for high-level gentamicin resistance in E. faecium isolates. Native crystals of this enzyme have been prepared and preliminary X-ray diffraction experiments have been undertaken. Bacterial resistance to the aminoglycoside antibiotics is primarily the result of deactivation of the drugs. Three families of enzymes are responsible for this activity, with one such family being the aminoglycoside phosphotransferases (APHs). The gene encoding one of these enzymes, APH(2′′)-Ib, has been cloned and the protein (comprising 299 amino-acid residues) expressed in Escherichia coli, purified and crystallized in the presence of 16%(w/v) PEG 3350 and gentamicin. The crystals belong to the monoclinic space group P2{sub 1}, with approximate unit-cell parameters a = 79.7, b = 58.8, c = 81.4 Å, β = 98.4°, and preliminary X-ray diffraction analysis is consistent with the presence of two molecules in the asymmetric unit. Synchrotron diffraction data to approximately 2.65 Å resolution were collected from a native APH(2′′)-Ib crystal at beamline BL9-2 at SSRL (Stanford, CA, USA). Selenium-substituted crystals have also been produced and structure determination is proceeding.

  20. Crystallization and preliminary X-ray diffraction analysis of myotoxin I, a Lys49-phospholipase A{sub 2} from Bothrops moojeni

    Energy Technology Data Exchange (ETDEWEB)

    Marchi-Salvador, D. P. [Departamento de Física e Biofísica-IB, UNESP, CP 510, CEP 18618-000, Botucatu-SP (Brazil); Silveira, L. B.; Soares, A. M. [Departamento de Biotecnologia, UNAERP, Ribeirão Preto/SP (Brazil); Fontes, M. R. M., E-mail: fontes@ibb.unesp.br [Departamento de Física e Biofísica-IB, UNESP, CP 510, CEP 18618-000, Botucatu-SP (Brazil)

    2005-10-01

    A new myotoxic Lys49-phospholipase from B. moojeni has been crystallized and X-ray diffraction data were collected to 2.18 Å resolution. Preliminary analysis indicates the presence of four molecules in the asymmetric unit, leading to a possible new oligomeric structure for Lys49-PLA{sub 2}s. A new myotoxic Lys49-phospholipase A{sub 2} isolated from Bothrops moojeni snake venom has been crystallized. The crystals diffracted to 2.18 Å resolution using a synchrotron-radiation source and belong to space group C2. The unit-cell parameters are a = 56.8, b = 125.0, c = 64.7 Å, β = 105.5°. Preliminary analysis indicates the presence of four molecules in the asymmetric unit. This may suggest a new quaternary structure for this Lys49-phospholipase A{sub 2} in contrast to the dimeric and monomeric structures solved so far for this class of proteins.

  1. Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    Simanshu, Dhirendra K.; Chittori, Sagar [Molecular Biophysics Unit, Indian Institute of Science, Bangalore (India); Savithri, H. S. [Department of Biochemistry, Indian Institute of Science, Bangalore (India); Murthy, M. R. N., E-mail: mrn@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore (India)

    2006-03-01

    S. typhimurium biodegradative threonine deaminase (TdcB), a member of the β-family of PLP-dependent enzymes, has been overexpressed, purified and crystallized in three different crystal forms using the hanging-drop vapour-diffusion method. Biodegradative threonine deaminase (TdcB) catalyzes the deamination of l-threonine to α-ketobutyrate, the first reaction in the anaerobic breakdown of l-threonine to propionate. Unlike the biosynthetic threonine deaminase, TdcB is insensitive to l-isoleucine and is activated by AMP. Here, the cloning of TdcB (molecular weight 36 kDa) from Salmonella typhimurium with an N-terminal hexahistidine affinity tag and its overexpression in Escherichia coli is reported. TdcB was purified to homogeneity using Ni–NTA affinity column chromatography and crystallized using the hanging-drop vapour-diffusion technique in three different crystal forms. Crystal forms I (unit-cell parameters a = 46.32, b = 55.30, c = 67.24 Å, α = 103.09, β = 94.70, γ = 112.94°) and II (a = 56.68, b = 76.83, c = 78.50 Å, α = 66.12, β = 89.16, γ = 77.08°) belong to space group P1 and contain two and four molecules of TdcB, respectively, in the asymmetric unit. Poorly diffracting form III crystals were obtained in space group C2 and based on the unit-cell volume are most likely to contain one molecule per asymmetric unit. Two complete data sets of resolutions 2.2 Å (crystal form I) and 1.7 Å (crystal form II) were collected at 100 K using an in-house X-ray source.

  2. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the aspartate transcarbamoylase domain of human CAD.

    Science.gov (United States)

    Ruiz-Ramos, Alba; Lallous, Nada; Grande-García, Araceli; Ramón-Maiques, Santiago

    2013-12-01

    Aspartate transcarbamoylase (ATCase) catalyzes the synthesis of N-carbamoyl-L-aspartate from carbamoyl phosphate and aspartate in the second step of the de novo biosynthesis of pyrimidines. In prokaryotes, the first three activities of the pathway, namely carbamoyl phosphate synthetase (CPSase), ATCase and dihydroorotase (DHOase), are encoded as distinct proteins that function independently or in noncovalent association. In animals, CPSase, ATCase and DHOase are part of a 243 kDa multifunctional polypeptide named CAD. Up-regulation of CAD is essential for normal and tumour cell proliferation. Although the structures of numerous prokaryotic ATCases have been determined, there is no structural information about any eukaryotic ATCase. In fact, the only detailed structural information about CAD is that it self-assembles into hexamers and trimers through interactions of the ATCase domains. Here, the expression, purification and crystallization of the ATCase domain of human CAD is reported. The recombinant protein, which was expressed in bacteria and purified with good yield, formed homotrimers in solution. Crystallization experiments both in the absence and in the presence of the inhibitor PALA yielded small crystals that diffracted X-rays to 2.1 Å resolution using synchrotron radiation. The crystals appeared to belong to the hexagonal space group P6(3)22, and Matthews coefficient calculation indicated the presence of one ATCase subunit per asymmetric unit, with a solvent content of 48%. However, analysis of the intensity statistics suggests a special case of the P21 lattice with pseudo-symmetry and possibly twinning.

  3. Crystallization and preliminary X-ray crystallographic analysis of a highly specific serpin from the beetle Tenebrio molitor

    Science.gov (United States)

    Park, Sun Hee; Piao, Shunfu; Kwon, Hyun-Mi; Kim, Eun-Hye; Lee, Bok Luel; Ha, Nam-Chul

    2010-01-01

    The Toll signalling pathway, which is crucial for innate immunity, is transduced in insect haemolymph via a proteolytic cascade consisting of three serine proteases. The proteolytic cascade is downregulated by a specific serine protease inhibitor (serpin). Recently, the serpin SPN48 was found to show an unusual specific reactivity towards the terminal serine protease, Spätzle-processing enzyme, in the beetle Tenebrio molitor. In this study, the mature form of SPN48 was overexpressed in Escherichia coli and purified. The purified SPN48 protein was crystallized using 14% polyethylene glycol 8000 and 0.1 M 2-(N-morpho­lino)ethanesulfonic acid pH 6.0 as the precipitant. The crystals diffracted X-rays to 2.1 Å resolution and were suitable for structure determination. The crystals belonged to space group P21. The crystal structure will provide information regarding how SPN48 achieves its unusual specificity for its target protease. PMID:20124722

  4. Crystallization of the glycogen-binding domain of the AMP-activated protein kinase β subunit and preliminary X-ray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Polekhina, Galina, E-mail: gpolekhina@svi.edu.au; Feil, Susanne C.; Gupta, Abhilasha [St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); O’Donnell, Paul [Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville 3010 (Australia); Stapleton, David; Parker, Michael W. [St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065 (Australia)

    2005-01-01

    The glycogen-binding domain of the AMP-activated kinase β subunit has been crystallized in the presence of β-cyclodextrin. The structure has been determined by single isomorphous replacement and threefold averaging using in-house X-ray data collected from selenomethionine-substituted protein. AMP-activated protein kinase (AMPK) is an intracellular energy sensor that regulates metabolism in response to energy demand and supply by adjusting the ATP-generating and ATP-consuming pathways. AMPK potentially plays a critical role in diabetes and obesity as it is known to be activated by metforin and rosiglitazone, drugs used for the treatment of type II diabetes. AMPK is a heterotrimer composed of a catalytic α subunit and two regulatory subunits, β and γ. Mutations in the γ subunit are known to cause glycogen accumulation, leading to cardiac arrhythmias. Recently, a functional glycogen-binding domain (GBD) has been identified in the β subunit. Here, the crystallization of GBD in the presence of β-cyclodextrin is reported together with preliminary X-ray data analysis allowing the determination of the structure by single isomorphous replacement and threefold averaging using in-house X-ray data collected from a selenomethionine-substituted protein.

  5. Expression, purification, crystallization and preliminary X-ray analysis of an NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Paul R.; Evans, Daniel; Greenwood, Jacqueline A.; Moody, Peter C. E., E-mail: pcem1@leicester.ac.uk [Henry Wellcome Laboratories for Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN (United Kingdom)

    2008-08-01

    Glyceraldehyde-3-phosphate dehydrogenase A has been cloned, expressed and purified. Apoprotein crystals have been grown which diffracted to 1.75 Å resolution and belonged to space group P2{sub 1}; holo crystals were grown in the presence of NADP, diffracted to 2.6 Å resolution and belonged to space group P3{sub 2}. The classical glycolytic pathway contains an NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, with NADP-dependent forms reserved for photosynthetic organisms and archaea. Here, the cloning, expression, purification, crystallization and preliminary X-ray analysis of an NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Helicobacter pylori is reported; crystals of the protein were grown both in the presence and the absence of NADP.

  6. Crystallization and preliminary X-ray crystallographic studies of glutaredoxin 2 from Saccharomyces cerevisiae in different oxidation states

    Energy Technology Data Exchange (ETDEWEB)

    Discola, Karen Fulan; Oliveira, Marcos Antonio de; Monteiro Silva, Gustavo [Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP (Brazil); Barcena, José Antonio; Porras, Pablo; Padilla, Alicia [Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio ‘Severo Ochoa’, Universidad de Córdoba, 14071 Córdoba (Spain); Netto, Luis Eduardo Soares [Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP (Brazil); Guimarães, Beatriz Gomes, E-mail: beatriz@lnls.br [Laboratório Nacional de Luz Síncrotron, CP 6192, CEP 13084-971, Campinas, SP (Brazil); Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP (Brazil)

    2005-04-01

    Glutaredoxin 2 (Grx2) from S. cerevisiae was expressed, purified and crystallized using the hanging-drop vapour-diffusion method. Crystals were obtained from protein treated with t-butyl hydroperoxide and from a sample not submitted to pre-treatment. Both crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2, with very similar unit-cell parameters, and diffraction data were collected to 2.05 and 2.15 Å resolution, respectively. Glutaredoxins are small (9–12 kDa) heat-stable proteins that are highly conserved throughout evolution; the glutaredoxin active site (Cys-Pro-Tyr-Cys) is conserved in most species. Five glutaredoxin genes have been identified in Saccharomyces cerevisiae; however, Grx2 is responsible for the majority of oxidoreductase activity in the cell, suggesting that its primary function may be the detoxification of mixed disulfides generated by reactive oxygen species (ROS). Recombinant Grx2 was expressed in Escherichia coli as a 6×His-tagged fusion protein and purified by nickel-affinity chromatography. Prior to crystallization trials, the enzyme was submitted to various treatments with reducing agents and peroxides. Crystals suitable for X-ray diffraction experiments were obtained from untreated protein and protein oxidized with t-butyl hydroperoxide (10 mM). Complete data sets were collected to resolutions 2.15 and 2.05 Å for untreated and oxidized Grx2, respectively, using a synchrotron-radiation source. The crystals belong to space group P4{sub 1}2{sub 1}2, with similar unit-cell parameters.

  7. Expression, purification, crystallization and preliminary X-ray characterization of the GRP carbohydrate-recognition domain from Homo sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Dongwen; Sun, Jianping; Zhao, Wei; Zhang, Xiao; Shi, Yunyu; Teng, Maikun, E-mail: mkteng@ustc.edu.cn; Niu, Liwen, E-mail: mkteng@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Dong, Yuhui; Liu, Peng [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100039 (China); Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China)

    2006-05-01

    The CRD domain of GRP from H. sapiens has been expressed, purified and crystallized and X-ray diffraction data have been collected to a resolution of 2.0 Å. Galectins are a family of animal lectins which share similar carbohydrate-recognition domains (CRDs) and an affinity for β-galactosides. A novel human galectin-related protein named GRP (galectin-related protein; previously known as HSPC159) comprises only one conserved CRD with 38 additional N-terminal residues. The C-terminal fragment of human GRP (GRP-C; residues 38–172) containing the CRD has been expressed and purified. The protein was crystallized using the hanging-drop vapour-diffusion method from a solution containing 2% PEG 400 and 2M ammonium sulfate in 100 mM Tris–HCl buffer pH 7.5. Diffraction data were collected to a resolution limit of 2.0 Å at beamline 3W1A of Beijing Synchrotron Radiation Facility at 100 K. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 123.07, b = 96.67, c = 61.56 Å, β = 118.72°. The estimated Matthews coefficient was 2.6 Å{sup 3} Da{sup −1}, corresponding to 51.8% solvent content.

  8. Crystallization and preliminary X-ray analysis of the haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58.

    Science.gov (United States)

    Mase, Tomoko; Yabuki, Hideya; Okai, Masahiko; Ohtsuka, Jun; Imai, Fabiana Lica; Nagata, Yuji; Tanokura, Masaru

    2012-06-01

    Haloalkane dehalogenases are enzymes that catalyze the hydrolytic reaction of a wide variety of haloalkyl substrates to form the corresponding alcohol and hydrogen halide products. DatA from Agrobacterium tumefaciens C58 is a haloalkane dehalogenase that has a unique pair of halide-binding residues, asparagine (Asn43) and tyrosine (Tyr109), instead of the asparagine and tryptophan that are conserved in other members of the subfamily. DatA was expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with a reservoir solution consisting of 0.1 M CHES pH 8.6, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate, 0.01 M barium chloride. X-ray diffraction data were collected to 1.70 Å resolution. The space group of the crystal was determined as the primitive tetragonal space group P422, with unit-cell parameters a = b = 123.7, c = 88.1 Å. The crystal contained two molecules in the asymmetric unit.

  9. Crystallization and preliminary X-ray characterization of arylamine N-acetyltransferase C (BanatC) from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Pluvinage, Benjamin [Laboratoire de Cytophysiologie et Toxicologie Cellulaire (EA 1553), Université Paris Diderot-Paris 7, 75005 Paris (France); Li de la Sierra-Gallay, Inés [Centre National de la Recherche (CNRS FRC550), Institut de Biologie Physico-Chimique, 75005 Paris (France); Martins, Marta; Ragunathan, Nilusha [Laboratoire de Cytophysiologie et Toxicologie Cellulaire (EA 1553), Université Paris Diderot-Paris 7, 75005 Paris (France); Dupret, Jean-Marie; Rodrigues-Lima, Fernando, E-mail: rlima@ext.jussieu.fr [Laboratoire de Cytophysiologie et Toxicologie Cellulaire (EA 1553), Université Paris Diderot-Paris 7, 75005 Paris (France); UFR de Biochimie, Université Paris Diderot-Paris 7, 75005 Paris (France)

    2007-10-01

    Bacillus anthracis arylamine N-acetyltransferase C (BanatC) is an enzyme that metabolizes the drug sulfamethoxazole. Crystals of the purified enzyme that diffract at 1.95 Å are reported. The arylamine N-acetyltransferase (NAT) enzymes are xenobiotic metabolizing enzymes that have been found in a large range of eukaryotes and prokaryotes. These enzymes catalyse the acetylation of arylamine drugs and/or pollutants. Recently, a Bacillus anthracis NAT isoform (BanatC) has been cloned and shown to acetylate the sulfonamide antimicrobial sulfamethoxazole (SMX). Subsequently, it was shown that BanatC contributes to the resistance of this bacterium to SMX. Here, the crystallization and the X-ray characterization of BanatC (Y38F mutant) are reported. The crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 53.70, c = 172.40 Å, and diffract to 1.95 Å resolution on a synchrotron source.

  10. Crystallization and preliminary X-ray analysis of l-methionine γ-lyase 1 from Entamoeba histolytica

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Dan [Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052 (Japan); Center for Integrated Medical Research, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 (Japan); Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511 (Japan); Karaki, Tsuyoshi; Shimizu, Akira; Kamei, Kaeko; Harada, Shigeharu, E-mail: harada@kit.ac.jp [Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585 (Japan); Nozaki, Tomoyoshi [Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511 (Japan); Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640 (Japan); Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052 (Japan)

    2008-08-01

    l-Methionine γ-lyase 1, a key enzyme in sulfur-containing amino-acid degradation, from the protozoan parasite E. histolytica was crystallized in a form suitable for X-ray structure analysis. l-Methionine γ-lyase (MGL) is a pyridoxal phosphate-dependent enzyme that is involved in the degradation of sulfur-containing amino acids. MGL is an attractive drug target against amoebiasis because the mammalian host of its causative agent Entamoeba histolytica lacks MGL. For the development of anti-amoebic agents based on the structure of MGL, one of two MGL isoenzymes (EhMGL1) was crystallized in the monoclinic space group P2{sub 1}, with unit-cell parameters a = 99.12, b = 85.38, c = 115.37 Å, β = 101.82°. The crystals diffract to beyond 2.0 Å resolution. The presence of a tetramer in the asymmetric unit (4 × 42.4 kDa) gives a Matthews coefficient of 2.8 Å{sup 3} Da{sup −1} and a solvent content of 56%. The structure was solved by the molecular-replacement method and structure refinement is now in progress.

  11. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of universal stress protein F (YnaF) from Salmonella typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    Sagurthi, Someswar Rao; Panigrahi, Rashmi Rekha; Gowda, Giri [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012 (India); Savithri, H. S. [Department of Biochemistry, Indian Institute of Science, Bangalore 560012 (India); Murthy, M. R. N., E-mail: mrn@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012 (India)

    2007-11-01

    The cloning, purification and crystallization of YnaF from S. typhimurium are reported along with preliminary X-ray crystallographic studies. The universal stress protein UspF (YnaF) is a small cytoplasmic bacterial protein. The expression of stress proteins is enhanced when cells are exposed to heat shock, nutrition starvation and certain other stress-inducing agents. YnaF promotes cell survival during prolonged exposure to stress and may activate a general mechanism for stress endurance. This manuscript reports preliminary crystallographic studies on YnaF from Salmonella typhimurium. The gene coding for YnaF was cloned and overexpressed and the protein was purified by Ni–NTA affinity chromatography. Purified YnaF was crystallized using vapour-diffusion and microbatch methods. The crystals belong to space group P2{sub 1}, with unit-cell parameters a = 37.51, b = 77.18, c = 56.34 Å, β = 101.8°. A data set was collected to 2.5 Å resolution with 94.6% completeness using an image-plate detector system mounted on a rotating-anode X-ray generator. Attempts to determine the structure are in progress.

  12. Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8.

    Science.gov (United States)

    Matsumoto, Ami; Shimizu, Yoshihiro; Takemoto, Chie; Ueda, Takuya; Uchiumi, Toshio; Ito, Kosuke

    2013-03-01

    Peptidyl-tRNA is produced from the ribosome as a result of aborted translation. Peptidyl-tRNA hydrolase cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, to recycle tRNA for further rounds of protein synthesis. In this study, peptidyl-tRNA hydrolase from Thermus thermophilus HB8 (TthPth) was crystallized using 2-methyl-2,4-pentanediol as a precipitant. The crystals belonged to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a=47.45, b=53.92, c=58.67 Å, and diffracted X-rays to atomic resolution (beyond 1.0 Å resolution). The asymmetric unit is expected to contain one TthPth molecule, with a solvent content of 27.13% (VM=1.69 Å3 Da(-1)). The structure is being solved by molecular replacement.

  13. Crystallization and preliminary X-ray crystallographic analysis of BxlE, a xylobiose transporter from Streptomyces thermoviolaceus OPC-520

    Science.gov (United States)

    Seike, Kiho; Sato, Junji; Tomoo, Koji; Ishida, Toshimasa; Yamano, Akihito; Ikenishi, Sadao; Miyamoto, Katsushiro; Tsujibo, Hiroshi

    2007-01-01

    Together with the integral membrane proteins BxlF and BxlG, BxlE isolated from Streptomyces thermoviolaceus OPC-520 forms an ATP-binding cassette (ABC) transport system that mediates the uptake of xylan. To clarify the structural basis of sugar binding by BxlE at the atomic level, recombinant BxlE was crystallized using the hanging-drop vapour-diffusion method at 290 K. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 44.63, b = 63.27, c = 66.40 Å, β = 103.05°, and contained one 48 kDa molecule per asymmetric unit (V M = 1.96 Å3 Da−1). Diffraction data collected to a resolution of 1.65 Å using a rotating-anode X-ray source gave a data set with an overall R merge of 2.6% and a completeness of 91.3%. A data set from a platinum derivative is being used for phasing by the SAD method. PMID:17620710

  14. Crystallization and preliminary X-ray diffraction analysis of BipD, a virulence factor from Burkholderia pseudomallei

    Energy Technology Data Exchange (ETDEWEB)

    Knight, M. J.; Ruaux, A.; Mikolajek, H.; Erskine, P. T.; Gill, R.; Wood, S. P. [School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX (United Kingdom); Wood, M. [Institute of Animal Health, Division of Environmental Microbiology, Institute for Animal Health, Compton Laboratory, Berkshire RG20 7NN (United Kingdom); Cooper, J. B., E-mail: j.b.cooper@soton.ac.uk [School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX (United Kingdom)

    2006-08-01

    BipD is likely to be a component of a type-III protein secretion system (TTSS) in B. pseudomallei. Native and selenomethionyl-BipD proteins have been expressed and crystals have been obtained which diffract to 2.1 Å. Burkholderia pseudomallei, the causative agent of melioidosis, possesses a protein-secretion apparatus that is similar to those found in Salmonella and Shigella. A major function of these secretion systems is to secrete virulence-associated proteins into target cells of the host organism. The BipD gene of B. pseudomallei encodes a secreted virulence factor that is similar in sequence and most likely functionally analogous to IpaD from Shigella and SipD from Salmonella. Thus, the BipD protein is likely to be a component of a type III protein-secretion system (TTSS) in B. pseudomallei. Proteins in the same class as BipD, such as IpaD and SipD, are thought to act as extracellular chaperones to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and might even link the translocon pore with the secretion needle. There is evidence that the translocator proteins also bind an integrin which stimulates actin-mediated insertion of the bacterium into the host-cell membrane. Native BipD has been crystallized in a monoclinic crystal form that diffracts X-rays to 2.5 Å resolution. BipD protein which incorporates selenomethionine (SeMet-BipD) has also been expressed and forms crystals which diffract to a higher resolution of 2.1 Å.

  15. Crystallization and preliminary X-ray diffraction analysis of P30, the transmembrane domain of pertactin, an autotransporter from Bordetella pertussis

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Yanshi; Black, Isobel; Roszak, Aleksander W.; Isaacs, Neil W., E-mail: n.isaacs@chem.gla.ac.uk [Department of Chemistry and WestChem, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom)

    2007-07-01

    P30, the transmembrane C-terminal domain of pertactin from B. pertussis has been crystallized after refolding in vitro. Preliminary X-ray crystallographic data are reported. P30, the 32 kDa transmembrane C-terminal domain of pertactin from Bordetella pertussis, is supposed to form a β-barrel inserted into the outer membrane for the translocation of the passenger domain. P30 was cloned and expressed in inclusion bodies in Escherichia coli. After refolding and purification, the protein was crystallized using the sitting-drop vapour-diffusion method at 292 K. The crystals diffract to a resolution limit of 3.5 Å using synchrotron radiation and belong to the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 123.27, c = 134.43 Å.

  16. Expression, purification, crystallization and preliminary X-ray analysis of an NAD-dependent glyceraldehyde-3-phosphate dehydrogenase from Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Paul R.; Mohammad, Shabaz; Melrose, Helen J.; Moody, Peter C. E., E-mail: pcem1@leicester.ac.uk [Henry Wellcome Laboratories for Structural Biology, University of Leicester, Leicester LE1 9HN (United Kingdom)

    2008-08-01

    Glyceraldehyde-3-phosphate dehydrogenase B from H. pylori has been cloned, expressed, purified and crystallized in the presence of NAD. Crystals of GAPDHB diffracted to 2.8 Å resolution and belonged to space group P6{sub 5}22, with unit-cell parameters a = b = 166.1, c = 253.1 Å. Helicobacter pylori is a dangerous human pathogen that resides in the upper gastrointestinal tract. Little is known about its metabolism and with the onset of antibiotic resistance new treatments are required. In this study, the expression, purification, crystallization and preliminary X-ray diffraction of an NAD-dependent glyceraldehyde-3-phosphate dehydrogenase from H. pylori are reported.

  17. Expression, Crystallization and Preliminary X-ray Diffraction Analyses of Med-ORF10 in the Biosynthetic Pathway of an Antitumor Antibiotic Medermycin.

    Science.gov (United States)

    Liu, Yanli; Liu, Shasha; Yang, Tingting; Guo, Xiaoxia; Jiang, Yali; Zahid, Kashif Rafiq; Liu, Ke; Liu, Jinlin; Yang, Jihong; Zhao, Haobin; Yang, Yi; Li, Aiying; Qi, Chao

    2015-12-01

    Medermycin, as a prominent member of benzoisochromanequinones, possesses strong antitumor activity and is biosynthesized under the control of a 29-ORF-containing biosynthetic gene cluster. Most of ORFs in this gene cluster have not been characterized, including a small protein encoding gene med-ORF10, proposed to play a regulatory role in biosynthesis of medermycin in an unknown mode. In this study, we reported the expression, protein preparation, crystallization and preliminary X-ray diffraction analyses of Med-ORF10 of the wild type Streptomyces strain. Firstly, we cloned and overexpressed med-ORF10 in Escherichia coli and purified the protein with 98% purity and 3 mg/L yield. Then, we crystallized the protein at concentration of 20 mg/mL in condition 22% PEG 3350, 0.2 M magnesium formate and collected the data at 1.78 Å resolution. Finally, we detected the expression of Med-ORF10 in Streptomyces by western blotting. In conclusion, this study confirmed the expression of Med-ORF10 protein in the wild-type strain of Streptomyces AM-7161 and collected the X-ray diffraction data of Med-ORF10 crystal at 1.78 Å resolution. These studies provide evidences for the functional Med-ORF10 protein in Streptomyces strains and facilitate our further investigation.

  18. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-β-1,4-glucanase from glycoside hydrolase family 12.

    Science.gov (United States)

    Segato, Fernando; Berto, Gabriela L; Ares de Araújo, Evandro; Muniz, João Renato; Polikarpov, Igor

    2014-02-01

    Endoglucanases are important enzymes that are involved in the modification and degradation of cellulose. Filamentous fungi such as Aspergillus terreus are effective biomass degraders in nature owing to their capacity to produce an enzymatic arsenal of glycoside hydrolases, including endoglucanase from glycoside hydrolase family 12 (GH12). The A. terreus GH12 endoglucanase was cloned and overexpressed in A. nidulans, purified and crystallized. A single crystal was obtained from a solution consisting of 2 M ammonium sulfate, 5%(v/v) 2-propanol. X-ray diffraction data were collected to a resolution of 1.85 Å using synchrotron radiation and a preliminary molecular-replacement solution was obtained in the trigonal space group P3(2)21. The unit-cell parameters were a = b = 103.24, c = 48.96 Å.

  19. A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1.

    Science.gov (United States)

    Collins, Brandon K; Tomanicek, Stephen J; Lyamicheva, Natasha; Kaiser, Michael W; Mueser, Timothy C

    2004-09-01

    Crystallization of protein and protein complexes is a multi-parametric problem that involves the investigation of a vast number of physical and chemical conditions. The buffers, salts and additives used to prepare the protein will be present in every crystallization condition. It is imperative that these conditions be defined prior to crystal screening since they will have a ubiquitous involvement in the crystal-growth experiments. This study involves the crystallization and preliminary analysis of the flap endonuclease-1 (FEN-1) DNA-repair enzyme from the crenarchaeal organism Aeropyrum pernix (Ape). Ape FEN-1 protein in a standard chromatography buffer had only a modest solubility and minimal success in crystallization trials. Using an ion/pH solubility screen, it was possible to dramatically increase the maximum solubility of the protein. The solubility-optimized protein produced large diffraction-quality crystals under multiple conditions in which the non-optimized protein produced only precipitate. Only minor adjustments of the conditions were required to produce single diffraction-quality crystals. The native Ape FEN-1 crystals diffract to 1.4 A resolution and belong to space group P6(1), with unit-cell parameters a = b = 92.8, c = 80.9 A, alpha = beta = 90, gamma = 120 degrees.

  20. Crystallization and preliminary X-ray diffraction analysis of a myotoxic Lys49-PLA{sub 2} from Bothrops jararacussu venom complexed with p-bromophenacyl bromide

    Energy Technology Data Exchange (ETDEWEB)

    Marchi-Salvador, D. P.; Fernandes, C. A. H. [Departamento de Física e Biofísica, Instituto de Biociências, UNESP, CP 510, CEP 18618-000, Botucatu-SP (Brazil); Amui, S. F.; Soares, A. M. [Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, FCFRP, USP, Ribeirão Preto/SP (Brazil); Fontes, M. R. M., E-mail: fontes@ibb.unesp.br [Departamento de Física e Biofísica, Instituto de Biociências, UNESP, CP 510, CEP 18618-000, Botucatu-SP (Brazil)

    2006-06-01

    A non-catalytic and myotoxic Lys49-PLA{sub 2} from B. jararacussu venom was crystallized with BPB inhibitor and X-ray diffraction data were collected. Preliminary analysis indicates that the ligand is bound to the His48 residue. Structure determination may provide insights into the myotoxic and cytotoxic mechanisms of Lys49-PLA{sub 2}s. For the first time, a non-catalytic and myotoxic Lys49-PLA{sub 2} (BthTX-I from Bothrops jararacussu venom) has been crystallized with BPB inhibitor. X-ray diffraction data were collected and electron-density calculations showed that the ligand is bound to the His48 residue. BthTX-I with His48 chemically modified by BPB shows strongly reduced myotoxic and cytotoxic activities. This suggests a biological correlation between the modification of His48, which is associated with catalytic activity of PLA{sub 2}s, and other toxicological activities of Lys49-PLA{sub 2}s.

  1. Crystallization and preliminary X-ray diffraction analysis of an anti-H(O) lectin from Lotus tetragonolobus seeds

    Energy Technology Data Exchange (ETDEWEB)

    Moreno, Frederico Bruno Mendes Batista; Martil, Daiana Evelin [Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil); Cavada, Benildo Sousa [BioMol-Lab UFC, Caixa Postal 6043, 60.455-970, Fortaleza-CE (Brazil); Azevedo, Walter Filgueira Jr de, E-mail: walter.junior@pucrs.br [Faculdade de Biociências-PUCRS, Av. Ipiranga 6681, Porto Alegre-RS, CEP 90619-900 (Brazil); Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil)

    2006-07-01

    The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. A complete structural data set was collected at 2.00 Å resolution using a synchrotron-radiation source. LTA crystals were found to be monoclinic, belonging to space group P2{sub 1}, with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 Å, α = γ = 90, β = 92°. Molecular replacement yielded a solution with a correlation coefficient and R factor of 34.4 and 51.6%, respectively. Preliminary analysis of the molecular-replacement solution indicates a new quaternary association in the LTA structure. Crystallographic refinement is under way.

  2. Crystallization and preliminary X-ray data collection of the Escherichia coli lipoproteins BamC, BamD and BamE

    OpenAIRE

    Albrecht, Reinhard; Zeth, Kornelius

    2010-01-01

    The cloning, purification and crystallization of the E. coli lipoproteins BamC, BamD and BamE is reported. X-ray diffraction data at high resolution were obtained for each of the proteins or protein domains.

  3. Crystallization and preliminary X-ray diffraction analysis of phospholipase A1 isolated from hornet (Vespa basalis) venom.

    Science.gov (United States)

    Chou, Chia-Cheng; Hou, Ming-Hon

    2008-12-01

    Phospholipase A(1) (PLA(1)) isolated from the black-bellied hornet (Vespa basalis) catalyzes the hydrolysis of emulsified phospholipids in addition to the potent haemolytic activity responsible for its lethal effect. In this study, the crystallization and preliminary crystallographic analysis of PLA(1) from hornet venom with a molecular weight of 32 kDa are reported. PLA(1) was crystallized at 277 K using PEG 4000 as precipitant and a 96.5% complete native data set was collected from a frozen crystal to 2.5 A resolution at 100 K with an overall R(merge) of 6.8%. The crystal belongs to the triclinic space group P1, with unit-cell parameters a = 57.2, b = 70.2, c = 81.6 A, alpha = 107.0, beta = 109.9, gamma = 100.9 degrees . In each asymmetric unit, three or four subunits of PLA(1) are present according to the calculation of the solvent content.

  4. Crystallization and preliminary X-ray diffraction analysis of two extracytoplasmic solute receptors of the DctP family from Bordetella pertussis

    Energy Technology Data Exchange (ETDEWEB)

    Rucktooa, Prakash; Huvent, Isabelle [UMR8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, 1 Rue du Professeur Calmette, BP 447, 59021 Lille CEDEX (France); IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); Antoine, Rudy; Lecher, Sophie; Jacob-Dubuisson, Françoise, E-mail: francoise.jacob@ibl.fr [IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); INSERM-U629, Lille (France); Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); Villeret, Vincent, E-mail: francoise.jacob@ibl.fr; Bompard, Coralie [UMR8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, 1 Rue du Professeur Calmette, BP 447, 59021 Lille CEDEX (France); IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France)

    2006-10-01

    Sample preparation, crystallization and preliminary X-ray analysis are reported for two B. pertussis extracytoplasmic solute receptors. DctP6 and DctP7 are two Bordetella pertussis proteins which belong to the extracytoplasmic solute receptors (ESR) superfamily. ESRs are involved in the transport of substrates from the periplasm to the cytosol of Gram-negative bacteria. DctP6 and DctP7 have been crystallized and diffraction data were collected using a synchrotron-radiation source. DctP6 crystallized in space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = 108.39, b = 108.39, c = 63.09 Å, while selenomethionyl-derivatized DctP7 crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 64.87, b = 149.83, c = 170.65 Å. The three-dimensional structure of DctP7 will be determined by single-wavelength anomalous diffraction, while the DctP6 structure will be solved by molecular-replacement methods.

  5. Cloning, overexpression, crystallization and preliminary X-ray crystallographic analysis of a slow-processing mutant of penicillin G acylase from Kluyvera citrophila.

    Science.gov (United States)

    Varshney, Nishant Kumar; Ramasamy, Sureshkumar; Brannigan, James A; Wilkinson, Anthony J; Suresh, C G

    2013-08-01

    Kluyvera citrophila penicillin G acylase (KcPGA) has recently attracted increased attention relative to the well studied and commonly used Escherichia coli PGA (EcPGA) because KcPGA is more resilient to harsh conditions and is easier to immobilize for the industrial hydrolysis of natural penicillins to generate the 6-aminopenicillin (6-APA) nucleus, which is the starting material for semi-synthetic antibiotic production. Like other penicillin acylases, KcPGA is synthesized as a single-chain inactive pro-PGA, which upon autocatalytic processing becomes an active heterodimer of α and β chains. Here, the cloning of the pac gene encoding KcPGA and the preparation of a slow-processing mutant precursor are reported. The purification, crystallization and preliminary X-ray analysis of crystals of this precursor protein are described. The protein crystallized in two different space groups, P1, with unit-cell parameters a = 54.0, b = 124.6, c = 135.1 Å, α = 104.1, β = 101.4, γ = 96.5°, and C2, with unit-cell parameters a = 265.1, b = 54.0, c = 249.2 Å, β = 104.4°, using the sitting-drop vapour-diffusion method. Diffraction data were collected at 100 K and the phases were determined using the molecular-replacement method. The initial maps revealed electron density for the spacer peptide.

  6. Crystallization and preliminary X-ray crystallographic investigations on a βγ-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Aravind, Penmatsa; Rajini, Bheemreddy; Sharma, Yogendra; Sankaranarayanan, Rajan, E-mail: sankar@ccmb.res.in [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India)

    2006-03-01

    The crystallization and preliminary X-ray diffraction analysis of AIM1g1, a βγ-crystallin domain of absent in melanoma (AIM1) protein from H. sapiens, is reported. AIM1g1 is a single βγ-crystallin domain from the protein absent in melanoma 1 (AIM1), which appears to play a role in the suppression of melanomas. This domain is known to bind calcium and its structure would help in identifying calcium-coordinating sites in vertebrate crystallins, which have hitherto been believed to have lost this ability during evolution. Crystallization of this domain was performed by the hanging-drop vapour-diffusion method. Crystals diffracted to a maximum resolution of 1.86 Å and were found to belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 54.98, c = 59.73 Å. Solvent-content analysis indicated the presence of one monomer per asymmetric unit.

  7. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analyses of threonyl-tRNA synthetase editing domain from Aeropyrum pernix.

    Science.gov (United States)

    Ahmad, Sadeem; Sravankumar, Antony S K; Kruparani, Shobha P; Sankaranarayanan, Rajan

    2012-11-01

    The proofreading function of aminoacyl-tRNA synthetases is crucial in maintaining the fidelity of protein synthesis. Most archaeal threonyl-tRNA synthetases (ThrRSs) possess a unique proofreading domain unrelated to their eukaryotic/bacterial counterpart. The crystal structure of this domain from the archaeon Pyrococcus abysii in complex with its cognate and noncognate substrate analogues had given insights into its catalytic and discriminatory mechanisms. To probe further into the mechanistic and evolutionary aspects of this domain, work has been extended to another archaeon Aeropyrum pernix. The organism possesses two proteins corresponding to threonyl-tRNA synthetase, i.e. ThrRS1 and ThrRS2, encoded by two different genes, thrS1 and thrS2, respectively. ThrRS1 is responsible for aminoacylation and ThrRS2 for proofreading activity. Here the purification, crystallization and preliminary X-ray crystallographic investigation of the N-terminal proofreading domain of ThrRS2 from A. pernix is reported. The crystals belong to either the P4(1)2(1)2 or P4(3)2(1)2 space group and consist of one monomer per asymmetric unit.

  8. Expression, crystallization and preliminary X-ray crystallographic analysis of XometC, a cystathionine γ-lyase-like protein from Xanthomonas oryzae pv. oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Phuong-Thuy Ho; Kim, Jin-Kwang [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Kim, Hyesoon [Major in Life Science, College of Natural Sciences, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743 (Korea, Republic of); Jung, Junho [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Ahn, Yeh-Jin [Major in Life Science, College of Natural Sciences, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743 (Korea, Republic of); Kim, Jeong-Gu; Lee, Byoung-Moo [Microbial Genetics Division, National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration (RDA), Suwon 441-707 (Korea, Republic of); Kang, Hee-Wan, E-mail: kanghw2@hknu.ac.kr [Graduate School of Biotechnology and Information, Hankyong National University, Ansung 456-749 (Korea, Republic of); Kang, Lin-Woo, E-mail: kanghw2@hknu.ac.kr [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of)

    2008-08-01

    XometC, a cystathionine γ-lyase-like protein from X. oryzae pv. oryzae and an antibacterial drug-target protein against bacterial blight, was cloned, purified and crystallized. Preliminary X-ray crystallographic analysis of XometC crystals was carried out. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice (Oryza sativa L.), one of the most devastating diseases of rice in most rice-growing countries. XometC, a cystathionine γ-lyase (CGL) like protein that is an antibacterial drug-target protein against Xoo, was cloned, expressed, purified and crystallized. CGL catalyzes the second step in the reverse-transsulfuration pathway, which is essential for the metabolic interconversion of the sulfur-containing amino acids cysteine and methionine. Crystals of two different shapes, plate-shaped and pyramid-shaped, diffracted to 2.9 and 3.2 Å resolution and belonged to the primitive orthogonal space group P2{sub 1}2{sub 1}2{sub 1} and the tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = 73.0, b = 144.9, c = 152.3 Å and a = b = 78.2, c = 300.7 Å, respectively. For the P2{sub 1}2{sub 1}2{sub 1} crystals, three or four monomers exist in the asymmetric unit with a corresponding V{sub M} of 3.02 or 2.26 Å{sup 3} Da{sup −1} and a solvent content of 59.3 or 45.7%. For the P4{sub 1} (or P4{sub 3}) crystals, four or five monomers exist in the asymmetric unit with a corresponding V{sub M} of 2.59 or 2.09 Å{sup 3} Da{sup −1} and a solvent content of 52.5 or 40.6%.

  9. Crystallization and preliminary X-ray diffraction study of a cell-wall invertase from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Verhaest, Maureen [Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, KU Leuven, E. Van Evenstraat 4, B-3000 Leuven (Belgium); Le Roy, Katrien [Laboratorium voor Moleculaire Plantenfysiologie, Faculteit Wetenschappen, Departement Biologie, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven (Belgium); Sansen, Stefaan [Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, KU Leuven, E. Van Evenstraat 4, B-3000 Leuven (Belgium); De Coninck, Barbara [Laboratorium voor Moleculaire Plantenfysiologie, Faculteit Wetenschappen, Departement Biologie, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven (Belgium); Lammens, Willem [Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, KU Leuven, E. Van Evenstraat 4, B-3000 Leuven (Belgium); Laboratorium voor Moleculaire Plantenfysiologie, Faculteit Wetenschappen, Departement Biologie, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven (Belgium); De Ranter, Camiel J. [Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, KU Leuven, E. Van Evenstraat 4, B-3000 Leuven (Belgium); Van Laere, André; Van den Ende, Wim [Laboratorium voor Moleculaire Plantenfysiologie, Faculteit Wetenschappen, Departement Biologie, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven (Belgium); Rabijns, Anja, E-mail: anja.rabijns@pharm.kuleuven.ac.be [Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, KU Leuven, E. Van Evenstraat 4, B-3000 Leuven (Belgium)

    2005-08-01

    Crystals suitable for structural analysis have been prepared from a cell-wall invertase from A. thaliana. Cell-wall invertase 1 (AtcwINV1), a plant protein from Arabidopsis thaliana which is involved in the breakdown of sucrose, has been crystallized in two different crystal forms. Crystal form I grows in space group P3{sub 1} or P3{sub 2}, whereas crystal form II grows in space group C222{sub 1}. Data sets were collected for crystal forms I and II to resolution limits of 2.40 and 2.15 Å, respectively.

  10. Crystallization and preliminary X-ray analysis of the 12S central subunit of transcarboxylase from Propionibacterium shermanii.

    Science.gov (United States)

    Wang, Y F; Hyatt, D C; Rivera, R E; Carey, P R; Yee, V C

    2001-02-01

    The hexameric 12S central subunit of transcarboxylase has been crystallized in both free and substrate-bound forms. The apo crystals belong to the cubic space group P4(2)32, with unit-cell parameters a = b = c = 188.5 A, and diffract to 3.5 A resolution. Crystals of two substrate-bound complexes, 12S with methylmalonyl CoA and 12S with malonyl CoA, are isomorphous and belong to space group C2, with unit-cell parameters a = 115.5, b = 201.4, c = 146.9 A, beta = 102.7 degrees. These crystals diffract to 1.9 A resolution with synchrotron radiation. Two useful heavy-atom phasing derivatives of methylmalonyl CoA-bound crystals have been obtained by co-crystallization or crystal soaking.

  11. Crystallization, preliminary X-ray crystallographic and cryo-electron microscopy analysis of a bifunctional enzyme fucokinase/L-fucose-1-P-guanylyltransferase from Bacteroides fragilis.

    Science.gov (United States)

    Cheng, Chongyun; Gu, Jianhua; Su, Jing; Ding, Wei; Yin, Jie; Liang, Wenguang; Yu, Xiaoxia; Ma, Jun; Wang, Peng George; Xiao, Zhicheng; Liu, Zhi-Jie

    2014-09-01

    Fucokinase/L-fucose-1-P-guanylyltransferase (FKP) is a bifunctional enzyme which converts L-fucose to Fuc-1-P and thence to GDP-L-fucose through a salvage pathway. The molecular weights of full-length FKP (F-FKP) and C-terminally truncated FKP (C-FKP, residues 300-949) are 105.7 and 71.7 kDa, respectively. In this study, both recombinant F-FKP and C-FKP were expressed and purified. Size-exclusion chromatography experiments and analytical ultracentrifugation results showed that both F-FKP and C-FKP are trimers. Native F-FKP protein was crystallized by the vapour-diffusion method and the crystals belonged to space group P212121 and diffracted synchrotron X-rays to 3.7 Å resolution. The crystal unit-cell parameters are a = 91.36, b = 172.03, c = 358.86 Å, α = β = γ = 90.00°. The three-dimensional features of the F-FKP molecule were observed by cryo-EM (cryo-electron microscopy). The preliminary cryo-EM experiments showed the F-FKP molecules as two parallel disc-shaped objects stacking together. Combining all results together, it is assumed that there are six FKP molecules in one asymmetric unit, which corresponds to a calculated Matthews coefficient of 2.19 Å(3) Da(-1) with 43.83% solvent content. These preliminary crystallographic and cryo-EM microscopy analyses provide basic structural information on FKP.

  12. Crystallization and preliminary X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex

    Energy Technology Data Exchange (ETDEWEB)

    Huet, Joëlle, E-mail: jhuet@ulb.ac.be [Laboratoire de Chimie Générale (CP 206/4), Institut de Pharmacie, Université Libre de Bruxelles (ULB), Campus de la Plaine, Boulevard du Triomphe, B-1050 Bruxelles (Belgium); Azarkan, Mohamed [Laboratoire de Chimie Générale (CP 609), Faculté de Médecine, Université Libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, B-1070 Bruxelles (Belgium); Looze, Yvan [Laboratoire de Chimie Générale (CP 206/4), Institut de Pharmacie, Université Libre de Bruxelles (ULB), Campus de la Plaine, Boulevard du Triomphe, B-1050 Bruxelles (Belgium); Villeret, Vincent [CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille 1-Université de Lille 2-Institut Pasteur de Lille, IFR142, 1 Rue du Professeur Calmette, F-59021 Lille (France); Wintjens, René, E-mail: jhuet@ulb.ac.be [Laboratoire de Chimie Générale (CP 206/4), Institut de Pharmacie, Université Libre de Bruxelles (ULB), Campus de la Plaine, Boulevard du Triomphe, B-1050 Bruxelles (Belgium)

    2008-05-01

    A chitinase isolated from the latex of the tropical species Carica papaya has been crystallized. The addition of N-acetyl-d-glucosamine to the crystallization solution has improved the diffraction quality resolution of the crystal to 1.8 Å resolution. A chitinase isolated from the latex of the tropical species Carica papaya has been purified to homogeneity and crystallized. This enzyme belongs to glycosyl hydrolase family 19 and exhibits exceptional resistance to proteolysis. The initially observed crystals, which diffracted to a resolution of 2.0 Å, were improved through modification of the crystallization protocol. Well ordered crystals were subsequently obtained using N-acetyl-d-glucosamine, the monomer resulting from the hydrolysis of chitin, as an additive to the crystallization solution. Here, the characterization of a chitinase crystal that belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 69.08, b = 44.79, c = 76.73 Å, β = 95.33° and two molecules per asymmetric unit, is reported. Diffraction data were collected to a resolution of 1.8 Å. Structure refinement is currently in progress.

  13. Purification, crystallization and preliminary X-ray diffraction of the G3BP1 NTF2-like domain

    DEFF Research Database (Denmark)

    Vognsen, Tina; Möller, Ingvar Rúnar; Kristensen, Ole

    2011-01-01

    The nuclear transport factor 2-like (NTF2-like) domain of human G3BP1 was subcloned, overexpressed in Escherichia coli and purified. Crystals were obtained using the hanging-drop vapour-diffusion method. Diffraction data were collected to 3.6 Å resolution using synchrotron radiation. The crystals...

  14. Cloning, expression, purification, crystallization and preliminary X-ray analysis of Thermus aquaticus succinyl-CoA synthetase

    Energy Technology Data Exchange (ETDEWEB)

    Joyce, Michael A. [Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7 (Canada); Brownie, Edward R.; Hayakawa, Koto; Fraser, Marie E., E-mail: frasm@ucalgary.ca [Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4 (Canada); Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7 (Canada)

    2007-05-01

    Attempts to crystallize succinyl-CoA synthetase from the thermophile T. aquaticus were thwarted by proteolysis of the β-subunit and preferential crystallization of a truncated form. Crystals of the full-length enzyme were grown after the purification protocol was modified to include frequent additions of protease inhibitors. Succinyl-CoA synthetase (SCS) is an enzyme of the citric acid cycle and is thus found in most species. To date, there are no structures available of SCS from a thermophilic organism. To investigate how the enzyme adapts to higher temperatures, SCS from Thermus aquaticus was cloned, overexpressed, purified and crystallized. Attempts to crystallize the enzyme were thwarted by proteolysis of the β-subunit and preferential crystallization of the truncated form. Crystals of full-length SCS were grown after the purification protocol was modified to include frequent additions of protease inhibitors. The resulting crystals, which diffract to 2.35 Å resolution, are of the protein in complex with Mn{sup 2+}-GDP.

  15. Crystallization and preliminary X-ray analysis of beta-alanine synthase from the yeast Saccharomyces kluyveri

    DEFF Research Database (Denmark)

    Dobritzsch, D.; Gojkovic, Zoran; Andersen, Birgit

    2003-01-01

    In eukaryotes and some bacteria, the third step of reductive pyrimidine catabolism is catalyzed by beta-alanine synthase (EC 3.5.1.6). Crystals of the recombinant enzyme from the yeast Saccharomyces kluyveri were obtained using sodium citrate as a precipitant. The crystals belong to space group P...

  16. Expression, purification, crystallization and preliminary X-ray diffraction analysis of α-11 giardin from Giardia lamblia

    Energy Technology Data Exchange (ETDEWEB)

    Pathuri, Puja; Nguyen, Emily Tam [Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 (United States); Luecke, Hartmut, E-mail: hudel@uci.edu [Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 (United States); Department of Physiology and Biophysics, University of California, Irvine, CA 92697 (United States); Department of Information and Computer Sciences, University of California, Irvine, CA 92697 (United States)

    2006-11-01

    α-11 giardin from the intestinal protozoan parasite, G. lamblia has been cloned, expressed, purified and crystallized under two different conditions and in two different space groups. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group and crystals obtained in the second condition diffracted to 2.93 Å and belong to a primitive monoclinic space group. α-11 Giardin, a protein from the annexin superfamily, is a 35.0 kDa protein from the intestinal protozoan parasite Giardia lamblia which triggers a form of diarrhea called giardiasis. Here, the cloning, expression, purification and the crystallization of α-11 giardin under two different conditions and in two different space groups is reported. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group, while crystals from the second condition, which included calcium in the crystallization solution, diffracted to 2.93 Å and belong to a primitive monoclinic space group. Determination of the detailed atomic structure of α-11 giardin will provide a better insight into its biological function and might establish whether this class of proteins is a potential drug target against giardiasis.

  17. Cloning, purification, crystallization and preliminary X-ray analysis of a chimeric NADPH-cytochrome P450 reductase.

    Science.gov (United States)

    Aigrain, Louise; Pompon, Denis; Truan, Gilles; Moréra, Solange

    2009-03-01

    NADPH-cytochrome P450 reductase (CPR) is the favoured redox partner of microsomal cytochromes P450. This protein is composed of two flavin-containing domains (FMN and FAD) connected by a structured linker. An active CPR chimera consisting of the yeast FMN and human FAD domains has been produced, purified and crystallized. The crystals belonged to the monoclinic space group C2 and contained one molecule per asymmetric unit. Molecular replacement was performed using the published rat and yeast structures as search models. The initial electron-density maps revealed that the chimeric enzyme had crystallized in a conformation that differed from those of previously solved structures.

  18. Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aeropyrum pernix K1.

    Science.gov (United States)

    D'Ambrosio, Katia; De Simone, Giuseppina; Pedone, Emilia; Rossi, Mosè; Bartolucci, Simonetta; Pedone, Carlo

    2005-03-01

    A protein disulfide oxidoreductase from the archaeon Aeropyrum pernix K1 has been overexpressed in Escherichia coli and crystallized at 298 K using the hanging-drop vapour-diffusion method. Crystals belong to the space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 90.59, b = 102.43, c = 128.96 A. A complete data set has been collected at the Elettra synchrotron source in Trieste to 1.93 A resolution using a single frozen crystal.

  19. Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1

    NARCIS (Netherlands)

    de Jong, RM; Rozeboom, HJ; Kalk, KH; Tang, Lixia; Janssen, DB; Dijkstra, BW

    Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals of the enantioselective halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1 have been obtained at room temperature from hanging-drop

  20. Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1

    NARCIS (Netherlands)

    Jong, René M. de; Rozeboom, Henriëtte J.; Kalk, Kor H.; Tang, Lixia; Janssen, Dick B.; Dijkstra, Bauke W.

    2002-01-01

    Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals of the enantioselective halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1 have been obtained at room temperature from hanging-drop

  1. Purification, crystallization and preliminary X-ray diffraction studies of d-tagatose 3-epimerase from Pseudomonas cichorii

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Hiromi; Yamada, Mitsugu [Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 (Japan); Nishitani, Takeyori; Takada, Goro; Izumori, Ken [Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795 (Japan); Kamitori, Shigehiro, E-mail: kamitori@med.kagawa-u.ac.jp [Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 (Japan)

    2007-02-01

    Recombinant d-tagatose 3-epimerase from P. cichorii was purified and crystallized. Diffraction data were collected to 2.5 Å resolution. d-Tagatose 3-epimerase (D-TE) from Pseudomonas cichorii catalyzes the epimerization of various ketohexoses at the C3 position. The epimerization of d-psicose has not been reported with epimerases other than P. cichorii D-TE and d-psicose 3-epimerase from Agrobacterium tumefaciens. Recombinant P. cichorii D-TE has been purified and crystallized. Crystals of P. cichorii D-TE were obtained by the sitting-drop method at room temperature. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 76.80, b = 94.92, c = 91.73 Å, β = 102.82°. Diffraction data were collected to 2.5 Å resolution. The asymmetric unit is expected to contain four molecules.

  2. Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Swairjo, Manal A., E-mail: swairjo@scripps.edu; Reddy, Robert R. [Departments of Chemistry and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, BCC-379, La Jolla, CA 92037 (United States); Lee, Bobby; Van Lanen, Steven G. [Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207 (United States); Brown, Shannon [Departments of Chemistry and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, BCC-379, La Jolla, CA 92037 (United States); Crécy-Lagard, Valérie de [Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611-0700 (United States); Iwata-Reuyl, Dirk [Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207 (United States); Schimmel, Paul [Departments of Chemistry and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, BCC-379, La Jolla, CA 92037 (United States)

    2005-10-01

    Structural informatics and modelling correctly predicted that substrate was required to obtain diffracting crystals of the first characterized nitrile oxidoreductase: the homododecameric QueF. QueF (MW = 19.4 kDa) is a recently characterized nitrile oxidoreductase which catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ{sub 0}) to 7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of the modified tRNA nucleoside queuosine. Initial crystals of homododecameric Bacillus subtilis QueF diffracted poorly to 8.0 Å. A three-dimensional model based on homology with the tunnel-fold enzyme GTP cyclohydrolase I suggested catalysis at intersubunit interfaces and a potential role for substrate binding in quaternary structure stabilization. Guided by this insight, a second crystal form was grown that was strictly dependent on the presence of preQ{sub 0}. This crystal form diffracted to 2.25 Å resolution.

  3. Crystallization and preliminary X-ray diffraction studies of maleylacetate reductase from Rhizobium sp. strain MTP-10005

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Tomomi; Goda, Yuko [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Yoshida, Masahiro; Oikawa, Tadao [Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680 (Japan); Hata, Yasuo, E-mail: hata@scl.kyoto-u.ac.jp [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2008-08-01

    Maleylacetate reductase from Rhizobium sp. strain MTP-10005 has been crystallized using the sitting-drop vapour-diffusion method and microseeding. The crystals contained one dimeric molecule per asymmetric unit and diffracted to 1.79 Å resolution. Maleylacetate reductase (EC 1.3.1.32), which catalyzes the reduction of maleylacetate to 3-oxoadipate, plays an important role in the aerobic microbial catabolism of resorcinol. The enzyme has been crystallized at 293 K by the sitting-drop vapour-diffusion method supplemented with a microseeding technique, using ammonium sulfate as the precipitating agent. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 56.85, b = 121.13, c = 94.09 Å, β = 101.48°, and contained one dimeric molecule in the asymmetric unit. It diffracted to 1.79 Å resolution.

  4. Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya

    Energy Technology Data Exchange (ETDEWEB)

    Azarkan, Mohamed [Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels (Belgium); Garcia-Pino, Abel [Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie and Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel (Belgium); Dibiani, Rachid [Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels (Belgium); Wyns, Lode; Loris, Remy, E-mail: reloris@vub.ac.be [Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie and Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel (Belgium); Baeyens-Volant, Danielle [Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels (Belgium)

    2006-12-01

    The Kunitz-type trypsin/chymotrypsin inhibitor isolated from C. papaya latex has been crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms are observed, diffracting to 2.6 and 1.7 Å. A Kunitz-type protease inhibitor purified from the latex of green papaya (Carica papaya) fruits was crystallized in the presence and absence of divalent metal ions. Crystal form I, which is devoid of divalent cations, diffracts to a resolution of 2.6 Å and belongs to space group P3{sub 1} or P3{sub 2}. This crystal form is a merohedral twin with two molecules in the asymmetric unit and unit-cell parameters a = b = 74.70, c = 78.97 Å. Crystal form II, which was grown in the presence of Co{sup 2+}, diffracts to a resolution of 1.7 Å and belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 44.26, b = 81.99, c = 140.89 Å.

  5. Crystallization and preliminary X-ray characterization of the relaxase domain of F factor TraI.

    Science.gov (United States)

    Larkin, Chris; Datta, Saumen; Nezami, Azin; Dohm, Julie A; Schildbach, Joel F

    2003-08-01

    Conjugative plasmids are capable of transferring a copy of themselves in single-stranded form from donor to recipient bacteria. Prior to transfer, one plasmid strand must be cleaved in a sequence-specific manner by a relaxase or mobilization protein. TraI is the relaxase for the conjugative plasmid F factor. A 36 kDa N-terminal fragment of TraI possesses the single-stranded DNA-binding and cleavage activity of the protein. Crystals of the 36 kDa TraI fragment in native and selenomethionine-labeled forms were grown by sitting-drop vapor-diffusion methods using PEG 1000 as the precipitant. Crystallization in the presence of chloride salts of magnesium and strontium was required to obtain crystals yielding high-resolution diffraction. To maintain high-resolution diffraction upon freezing, crystals had to be soaked in crystallization buffer with stepwise increases of ethylene glycol. The resulting crystals were trigonal and diffracted to a resolution of 3.1 A or better using synchrotron radiation.

  6. Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV)

    Energy Technology Data Exchange (ETDEWEB)

    Goulet, Adeline; Spinelli, Silvia; Campanacci, Valérie; Porciero, Sophie; Blangy, Stéphanie [Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9 (France); Garrett, Roger A. [Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University, Soelvgade 83H, DK1307 Copenhagen K (Denmark); Tilbeurgh, Herman van; Leulliot, Nicolas [Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris 11, Bâtiment 430, 91405 Orsay (France); Basta, Tamara; Prangishvili, David [Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 Rue du Dr Roux, 75724 Paris CEDEX 15 (France); Cambillau, Christian, E-mail: cambillau@afmb.univ-mrs.fr [Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9 (France)

    2006-09-01

    Crystals of S. islandicus filamentous virus (SIFV) protein 14 have been grown at 293 K. Crystals belong to space group P6{sub 2}22 or P6{sub 4}22 and diffract to a resolution of 2.95 Å. A large-scale programme has been embarked upon aiming towards the structural determination of conserved proteins from viruses infecting hyperthermophilic archaea. Here, the crystallization of protein 14 from the archaeal virus SIFV is reported. This protein, which contains 111 residues (MW 13 465 Da), was cloned and expressed in Escherichia coli with an N-terminal His{sub 6} tag and purified to homogeneity. The tag was subsequently cleaved and the protein was crystallized using PEG 1000 or PEG 4000 as a precipitant. Large crystals were obtained of the native and the selenomethionine-labelled protein using sitting drops of 100–300 nl. Crystals belong to space group P6{sub 2}22 or P6{sub 4}22, with unit-cell parameters a = b = 68.1, c = 132.4 Å. Diffraction data were collected to a maximum acceptable resolution of 2.95 and 3.20 Å for the SeMet-labelled and native protein, respectively.

  7. Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa

    Energy Technology Data Exchange (ETDEWEB)

    Taguchi, Chiho [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Taura, Futoshi [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Tamada, Taro; Shoyama, Yoshinari [Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Shoyama, Yukihiro; Tanaka, Hiroyuki [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Kuroki, Ryota, E-mail: kuroki.ryota@jaea.go.jp [Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Morimoto, Satoshi [Faculty of Pharmaceutical Sciences, Kyushu University (Japan)

    2008-03-01

    Polyketide synthase-1 from C. sativa has been crystallized. The crystal diffracted to 1.55 Å resolution with sufficient quality for further structure determination. Polyketide synthase-1 (PKS-1) is a novel type III polyketide synthase that catalyzes the biosynthesis of hexanoyl triacetic acid lactone in Cannabis sativa (Mexican strain). PKS-1 was overproduced in Escherichia coli, purified and finally crystallized in two different space groups. The crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M calcium acetate and 20%(w/v) polyethylene glycol 3350 diffracted to 1.65 Å resolution and belonged to space group P1, with unit-cell parameters a = 54.3, b = 59.3, c = 62.6 Å, α = 69, β = 81, γ = 80°. Another crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M sodium chloride and 20%(w/v) polyethylene glycol 3350 diffracted to 1.55 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 54.3, b = 110, c = 130 Å. These data will enable us to determine the crystal structure of PKS-1.

  8. Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase

    Energy Technology Data Exchange (ETDEWEB)

    Mauracher, Stephan Gerhard; Molitor, Christian [Universität Wien, Althanstrasse 14, 1090 Wien (Austria); Al-Oweini, Rami; Kortz, Ulrich [Jacobs University, PO Box 750 561, 28759 Bremen (Germany); Rompel, Annette, E-mail: annette.rompel@univie.ac.at [Universität Wien, Althanstrasse 14, 1090 Wien (Austria)

    2014-01-23

    Polyphenol oxidase 4 (PPO4) from the natural source A. bisporus was crystallized in its latent precursor form (pro-tyrosinase; Ser2–Thr565) using the 6-tungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}]·22H{sub 2}O as a crystallization additive. Tyrosinase exhibits catalytic activity for the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones. Owing to polymerization of these quinones, brown-coloured high-molecular-weight compounds called melanins are generated. The latent precursor form of polyphenol oxidase 4, one of the six tyrosinase isoforms from Agaricus bisporus, was purified to homogeneity and crystallized. The obtained crystals belonged to space group C121 (two molecules per asymmetric unit) and diffracted to 2.78 Å resolution. The protein only formed crystals under low-salt conditions using the 6-tungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}]·22H{sub 2}O as a co-crystallization agent.

  9. Crystallization and preliminary X-ray diffraction studies of θ-toxin (perfringolysin O), a pore-forming cytolysin of Clostridium perfringens

    Science.gov (United States)

    Sugahara, Mitsuaki; Sekino-Suzuki, Naoko; Ohno-Iwashita, Yoshiko; Miki, Kunio

    1996-10-01

    θ-Toxin (perfringolysin O), a cholesterol-binding, pore-forming cytolysin of Clostridium perfringens type A was crystallized by the vapor diffusion procedure using polyethyleneglycol 4000 and sodium chloride as precipitants in 2-(cyclohexylamino)ethanesulfonic acid (CHES) buffer at pH 9.5. The diffraction patterns of precession photographs indicated that the crystals belong to the orthorhombic system and the space group C222 1 with unit-cell dimensions of a = 47.7 Å, b = 182.0 Å and c = 175.8 Å. Assuming that the asymmetric unit contains one or two molecules (Mw 52 700), the Vm value is calculated as 3.6 or 1.8 Å 3/dalton, respectively. The crystals diffract X-rays to at least 3 Å resolution and are suitable for high resolution X-ray crystal structure determination.

  10. Crystallization and preliminary X-ray analysis of a RecB-family nuclease from the archaeon Pyrococcus abyssi

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Bin, E-mail: ren@csb.ki.se [Center for Structural Biochemistry, Karolinska Institute, NOVUM, S-141 57 Huddinge (Sweden); Kuhn, Joëlle; Meslet-Cladiere, Laurence; Myllykallio, Hannu [Université Paris-Sud, Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8621, F-91405 Orsay CEDEX (France); Ladenstein, Rudolf [Center for Structural Biochemistry, Karolinska Institute, NOVUM, S-141 57 Huddinge (Sweden)

    2007-05-01

    A RecB-like nuclease from the archaeon Pyrococcus abyssi was expressed, purified and crystallized. The crystals belong to the orthorhombic space group C222{sub 1} with a = 81.5, b = 159.8, c = 100.8 Å, and a native data set was collected to 2.65 Å resolution. Nucleases are required to process and repair DNA damage in living cells. One of the best studied nucleases is the RecB protein, which functions in Escherichia coli as a component of the RecBCD enzyme complex that amends double-strand breaks in DNA. Although archaea do not contain the RecBCD complex, a RecB-like nuclease from Pyrococcus abyssi has been cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method using polyethylene glycol 8000 as the precipitant. The crystals belong to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 81.5, b = 159.8, c = 100.8 Å. Self-rotation function and native Patterson map calculations revealed that there is a dimer in the asymmetric unit with its local twofold axis running parallel to the crystallographic twofold screw axis. The crystals diffracted to about 2 Å and a complete native data set was collected to 2.65 Å resolution.

  11. Crystallization and preliminary X-ray diffraction studies of two thermostable α-galactosidases from glycoside hydrolase family 36

    Science.gov (United States)

    Foucault, M.; Watzlawick, H.; Mattes, R.; Haser, R.; Gouet, P.

    2006-01-01

    α-Galactosidases from thermophilic organisms have gained interest owing to their applications in the sugar industry. The α-galactosidases AgaA, AgaB and AgaA A355E mutant from Geobacillus stearothermophilus have been overexpressed in Escherichia coli. Crystals of AgaB and AgaA A355E have been obtained by the vapour-diffusion method and synchrotron data have been collected to 2.0 and 2.8 Å resolution, respectively. Crystals of AgaB belong to space group I222 or I212121, with unit-cell parameters a = 87.5, b = 113.3, c = 161.6 Å. Crystals of AgaA A355E belong to space group P3121 or P3221, with unit-cell parameters a = b = 150.1, c = 233.2 Å. PMID:16511274

  12. Crystallization and preliminary X-ray analysis of beta-alanine synthase from the yeast Saccharomyces kluyveri.

    Science.gov (United States)

    Dobritzsch, Doreen; Gojković, Zoran; Andersen, Birgit; Piskur, Jure

    2003-07-01

    In eukaryotes and some bacteria, the third step of reductive pyrimidine catabolism is catalyzed by beta-alanine synthase (EC 3.5.1.6). Crystals of the recombinant enzyme from the yeast Saccharomyces kluyveri were obtained using sodium citrate as a precipitant. The crystals belong to space group P2(1) (unit-cell parameters a = 117.2, b = 77.1, c = 225.5 A, beta = 95.0 degrees ) and contain four homodimers per asymmetric unit. Data were collected to 2.7 A resolution. Introduction of heavy atoms into the crystal lattice induced a different set of unit-cell parameters (a = 61.0, b = 77.9, c = 110.1 A, beta = 97.2 degrees ) in the same space group P2(1), with only one homodimer per asymmetric unit.

  13. Preparation, crystallization and preliminary X-ray analysis of the methionine synthase (MetE) from Streptococcus mutans

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Tian-Min; Zhang, Xiao-Yan; Li, Lan-Fen; Liang, Yu-He, E-mail: liangyh@pku.edu.cn; Su, Xiao-Dong [National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871 (China); Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871 (China)

    2006-10-01

    Methionine synthase (MetE) from S. mutans was expressed, purified and crystallized. Diffraction data have been collected to 2.2 Å resolution. The Streptococcus mutans metE gene encodes methionine synthase (MetE), which catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to homocysteine in the last step of methionine synthesis. metE was cloned into pET28a and the gene product was expressed at high levels in the Escherichia coli strain BL21 (DE3). MetE was purified to homogeneity using Ni{sup 2+}-chelating chromatography followed by size-exclusion chromatography. Crystals of the protein were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.2 Å resolution. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 52.85, b = 99.48, c = 77.88 Å, β = 94.55°.

  14. Purification, crystallization and preliminary X-ray diffraction analysis of Cif, a virulence factor secreted by Pseudomonas aeruginosa.

    Science.gov (United States)

    Bahl, Christopher D; MacEachran, Daniel P; O'Toole, George A; Madden, Dean R

    2010-01-01

    The opportunistic pathogen Pseudomonas aeruginosa secretes a protein that triggers the accelerated degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells. This protein, which is known as the CFTR inhibitory factor (Cif), acts as a virulence factor and may facilitate airway colonization by P. aeruginosa. Based on sequence similarity Cif appears to be an epoxide hydrolase (EH), but it lacks several of the conserved features found in the active sites of canonical members of the EH family. Here, the crystallization of purified recombinant Cif by vapor diffusion is reported. The crystals formed in space group C2, with unit-cell parameters a = 167.4, b = 83.6, c = 88.3 A, beta = 100.6 degrees . The crystals diffracted to 2.39 A resolution on a rotating-anode source. Based on the calculated Matthews coefficient (2.2 A(3) Da(-1)), it appears that the asymmetric unit contains four molecules.

  15. Crystallization and preliminary X-ray analysis of cardiotoxic phospholipase A2 from Ophiophagus hannah (king cobra).

    Science.gov (United States)

    Wang, Z; Zhuang, M; Shu, Y; Zhang, H; Song, S; Lin, Z

    2001-05-01

    An acidic phospholipase A2 exhibiting cardiotoxicity, myotoxicity and anti-platelet activity was isolated from Ophiophagus hannah (king cobra) from Guangxi, China. It contains an unusual 'pancreatic loop'. The enzyme was purified to homogeneity and crystallized using polyethylene glycol and ethylene glycol as precipitants. The crystal belongs to space group C2, with unit-cell parameters a = 117.92, b = 62.94, c = 57.16 A, beta = 100.93 degrees. Diffraction data were collected to 2.6 A.

  16. Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom

    Energy Technology Data Exchange (ETDEWEB)

    Igarashi, Tomoko; Oishi, Yuko [Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565 (Japan); Araki, Satohiko [Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie 517-0004 (Japan); Mori, Hidezo [Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565 (Japan); Takeda, Soichi, E-mail: stakeda@ri.ncvc.go.jp [Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565 (Japan); Laboratory for Structural Biochemistry, Riken Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148 (Japan)

    2006-07-01

    Vascular apoptosis-inducing protein 1 (VAP1) and VAP2 from C. atrox venom were crystallized in variety of different crystal forms. Diffraction data sets were obtained to 2.5 and 2.15 Å resolution for VAP1 and VAP2, respectively. VAPs are haemorrhagic snake-venom toxins belonging to the reprolysin family of zinc metalloproteinases. In vitro, VAPs induce apoptosis specifically in cultured vascular endothelial cells. VAPs have a modular structure that bears structural homology to mammalian ADAMs (a disintegrin and metalloproteinases). VAP1 is a homodimer with a MW of 110 kDa in which the monomers are connected by a single disulfide bridge. VAP2 is homologous to VAP1 and exists as a monomer with a MW of 55 kDa. In the current study, several crystal forms of VAP1 and VAP2 were obtained using the vapour-diffusion method and diffraction data sets were collected using SPring-8 beamlines. The best crystals of VAP1 and VAP2 generated data sets to 2.5 and 2.15 Å resolution, respectively.

  17. Crystallization and preliminary X-ray diffraction studies of choline-binding protein F from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    Molina, Rafael [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); González, Ana; Moscoso, Miriam; García, Pedro [Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain); Stelter, Meike; Kahn, Richard [Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF, Laboratoire de Cristallographie Macromoléculaire, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX 1 (France); Hermoso, Juan A., E-mail: xjuan@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain)

    2007-09-01

    The modular choline-binding protein F (CbpF) from S. pneumoniae has been crystallized by the hanging-drop vapour-diffusion method. A SAD data set from a gadolinium-complex derivative has been collected to 2.1 Å resolution. Choline-binding protein F (CbpF) is a modular protein that is bound to the pneumococcal cell wall through noncovalent interactions with choline moieties of the bacterial teichoic and lipoteichoic acids. Despite being one of the more abundant proteins on the surface, along with the murein hydrolases LytA, LytB, LytC and Pce, its function is still unknown. CbpF has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality orthorhombic crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 49.13, b = 114.94, c = 75.69 Å. A SAD data set from a Gd-HPDO3A-derivatized CbpF crystal was collected to 2.1 Å resolution at the gadolinium L{sub III} absorption edge using synchrotron radiation.

  18. Crystallization and preliminary X-ray diffraction studies of two thermostable α-galactosidases from glycoside hydrolase family 36

    Energy Technology Data Exchange (ETDEWEB)

    Foucault, M. [Institut de Biologie et Chimie des Protéines, CNRS-UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07 (France); Watzlawick, H.; Mattes, R. [Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart (Germany); Haser, R.; Gouet, P., E-mail: p.gouet@ibcp.fr [Institut de Biologie et Chimie des Protéines, CNRS-UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07 (France)

    2006-02-01

    The α-galactosidases AgaA, AgaB and AgaA A355E mutant from Geobacillus stearothermophilus have been overexpressed in Escherichia coli. Crystals of AgaB and AgaA A355E have been obtained by the vapour-diffusion method and synchrotron data have been collected to 2.0 and 2.8 Å resolution, respectively. α-Galactosidases from thermophilic organisms have gained interest owing to their applications in the sugar industry. The α-galactosidases AgaA, AgaB and AgaA A355E mutant from Geobacillus stearothermophilus have been overexpressed in Escherichia coli. Crystals of AgaB and AgaA A355E have been obtained by the vapour-diffusion method and synchrotron data have been collected to 2.0 and 2.8 Å resolution, respectively. Crystals of AgaB belong to space group I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 87.5, b = 113.3, c = 161.6 Å. Crystals of AgaA A355E belong to space group P3{sub 1}21 or P3{sub 2}21, with unit-cell parameters a = b = 150.1, c = 233.2 Å.

  19. Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis

    Energy Technology Data Exchange (ETDEWEB)

    Vordtriede, Paul B.; Yoder, Marilyn D., E-mail: yoderm@umkc.edu [Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110 (United States)

    2008-07-01

    The acidic polygalacturonase PehA from A. vitis has been crystallized. A molecular-replacement solution indicated a right-handed parallel β-helix fold. Polygalacturonases are pectate-degrading enzymes that belong to glycoside hydrolase family 28 and hydrolyze the α-1,4 glycosidic bond between neighboring galacturonasyl residues of the homogalacturonan substrate. The acidic polygalacturonase PehA from Agrobacterium vitis was overexpressed in Escherichia coli, where it accumulated in the periplasmic fraction. It was purified to homogeneity via a two-step chromatography procedure and crystallized using the hanging-drop vapour-diffusion technique. PehA crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 52.387, b = 62.738, c = 149.165 Å, β = 89.98°. Crystals diffracted to 1.59 Å resolution and contained two molecules per asymmetric unit. An initial structure determination by molecular replacement indicated a right-handed parallel β-helix fold.

  20. Crystallization and preliminary X-ray diffraction analysis of the azoreductase PpAzoR from Pseudomonas putida MET94.

    Science.gov (United States)

    Correia, Bruno; Chen, Zhenjia; Mendes, Sónia; Martins, Lígia O; Bento, Isabel

    2011-01-01

    PpAzoR, an FMN-dependent NADPH azoreductase from Pseudomonas putida MET94, has been crystallized using the sitting-drop vapour-diffusion technique. The crystals diffracted to 1.6 Å resolution using synchrotron radiation and belonged to the orthorhombic space group F222, with unit-cell parameters a=72.1, b=95.5, c=146.1 Å. Data sets were collected from the native protein to 2.2 Å resolution using in-house equipment and to 1.6 Å resolution using synchrotron radiation and the three-dimensional structure was determined by the molecular-replacement method.

  1. Crystallization and preliminary X-ray diffraction analysis of thioredoxin peroxidase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1.

    Science.gov (United States)

    Nakamura, Tsutomu; Matsumura, Hiroyoshi; Inoue, Tsuyoshi; Kai, Yasushi; Uegaki, Koichi; Hagihara, Yoshihisa; Ataka, Mitsuo; Ishikawa, Kazuhiko

    2005-03-01

    Thioredoxin peroxidase is a member of the peroxiredoxin family and plays a dominant role in a hydrogen peroxide metabolism. A recombinant form of the hyperthermostable thioredoxin peroxidase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1, a polypeptide consisting of 250 amino acids, was purified. The C207S mutant protein was crystallized by the hanging-drop vapour-diffusion method using potassium sodium tartrate as the precipitant at 298 K. Diffraction data were collected and processed to 2.7 A resolution. The crystal belongs to space group P1, with unit-cell parameters a = 126.2, b = 126.3, c = 213.7 A, alpha = 80.4, beta = 80.3, gamma = 70.7 degrees. Calculation of the self-rotation function showed that the protein quaternary structure includes a fivefold axis and five twofold axes.

  2. Cloning, recombinant production, crystallization and preliminary X-ray diffraction studies of a family 84 glycoside hydrolase from Clostridium perfringens

    Energy Technology Data Exchange (ETDEWEB)

    Ficko-Blean, Elizabeth; Boraston, Alisdair B., E-mail: boraston@uvic.ca [Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6 (Canada)

    2005-09-01

    Crystallization of a family 84 glycoside hydrolase, a putative virulence factor, secreted by C. perfringens is reported. Clostridium perfringens is a ubiquitous environmental organism that is capable of causing a variety of diseases in mammals, including gas gangrene and necrotic enteritis in humans. The activity of a secreted hyaluronidase, attributed to the NagH protein, contributes to the pathogenicity of this organism. The family 84 catalytic module of one of the three homologues of NagH found in C. perfringens (ATCC 13124) has been cloned. The 69 kDa catalytic module of NagJ, here called GH84C, was overproduced in Escherichia coli and purified by immobilized metal-affinity chromatography (IMAC). Crystals belonging to space group I222 or I2{sub 1}2{sub 1}2{sub 1} with unit-cell parameters a = 130.39, b = 150.05, c = 155.43 Å were obtained that diffracted to 2.1 Å. Selenomethionyl crystals have also been produced, leading to the possibility of solving the phase problem by MAD using synchrotron radiation.

  3. Crystallization and preliminary X-ray analysis of enoyl-acyl carrier protein reductase (FabK) from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Jun, E-mail: jun-saito@meiji.co.jp; Yamada, Mototsugu; Watanabe, Takashi; Kitagawa, Hideo; Takeuchi, Yasuo [Pharmaceutical Research Center, Meiji Seika Kaisha Ltd, 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567 (Japan)

    2006-06-01

    Enoyl-acyl carrier protein (ACP) reductases are responsible for bacterial type II fatty-acid biosynthesis and are attractive targets for developing novel antibiotics. The S. pneumoniae enoyl-ACP reductase (FabK) was crystallized and selenomethionine MAD data were collected to 2 Å resolution. The enoyl-acyl carrier protein (ACP) reductase from Streptococcus pneumoniae (FabK; EC 1.3.1.9) is responsible for catalyzing the final step in each elongation cycle of fatty-acid biosynthesis. Selenomethionine-substituted FabK was purified and crystallized by the hanging-drop vapour-diffusion method at 277 K. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 50.26, b = 126.70, c = 53.63 Å, β = 112.46°. Diffraction data were collected to 2.00 Å resolution using synchrotron beamline BL32B2 at SPring-8. Two molecules were estimated to be present in the asymmetric unit, with a solvent content of 45.1%.

  4. Crystallization and Preliminary X-ray Analysis of Der f 2, a Potent Allergen Derived from the House Dust Mite

    Science.gov (United States)

    Roeber, Dana; Achari, Aniruddha; Takai, Toshiro; Okumura, Yasushi; Scott, David L.; Curreri, Peter (Technical Monitor)

    2002-01-01

    Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophugoides sp.) are particularly ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis, and asthma associated with allergic reactions to these arthropods are often caused by relatively small (125-129 amino acids) mite proteins of unclear biological function. Der f 2, a major allergen from the mite Dermatophagoides farinae, has been recombinantly expressed and characterized. The Der f 2 protein has been crystallized in our laboratory and a native data set collected at a synchrotron source. The crystals belong to the orthorhombic space group I422 with unit cell parameters of a = 95.2 Angstroms, b = 95.2 Angstroms, and c = 103.3 Angstroms. An essentially complete (97.2%) data set has been collected to 2.4 Angstroms. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the available NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pterovssinus) failed to reveal a creditable solution.

  5. Crystallization and preliminary X-ray diffraction analysis of Val57 mutants of the amyloidogenic protein human cystatin C

    Energy Technology Data Exchange (ETDEWEB)

    Orlikowska, Marta; Jankowska, Elzbieta; Borek, Dominika; Otwinowski, Zbyszek; Skowron, Piotr; Szymanska, Aneta (Gdansk); (UTSMC)

    2012-03-15

    Human cystatin C (hCC) is a low-molecular-mass protein (120 amino-acid residues, 13 343 Da) found in all nucleated cells. Its main physiological role is regulation of the activity of cysteine proteases. Biologically active hCC is a monomeric protein, but all crystallization efforts have resulted in a dimeric domain-swapped structure. Recently, two monomeric structures were reported for cystatin C variants. In one of them stabilization was achieved by abolishing the possibility of domain swapping by the introduction of an additional disulfide bridge connecting the two protein domains (Cys47-Cys69). In the second structure, reported by this group, the monomeric hCC fold was preserved by stabilization of the conformationally constrained loop (L1) by a single-amino-acid substitution (V57N). To further assess the influence of changes in the sequence and properties of loop L1 on the dimerization propensity of cystatin C, two additional hCC mutants were obtained: one with a residue favoured in {beta}-turns (V57D) and another with proline (V57P), a residue that is known to be a structural element that can rigidify but also broaden turns. Here, the expression, purification and crystallization of V57D and V57P variants of recombinant human cystatin C are described. Crystals were grown by the vapour-diffusion method. Several diffraction data sets were collected using a synchrotron source at the Advanced Photon Source, Argonne National Laboratory, Chicago, USA.

  6. Purification, Crystallization and Preliminary X-ray Diffraction Analysis of Cif, a Virulence Factor Secreted by Pseudomonas aeruginosa

    Energy Technology Data Exchange (ETDEWEB)

    Bahl, C.; MacEachran, D; O& apos; Toole, G; Madden, D

    2010-01-01

    The opportunistic pathogen Pseudomonas aeruginosa secretes a protein that triggers the accelerated degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells. This protein, which is known as the CFTR inhibitory factor (Cif), acts as a virulence factor and may facilitate airway colonization by P. aeruginosa. Based on sequence similarity Cif appears to be an epoxide hydrolase (EH), but it lacks several of the conserved features found in the active sites of canonical members of the EH family. Here, the crystallization of purified recombinant Cif by vapor diffusion is reported. The crystals formed in space group C2, with unit-cell parameters a = 167.4, b = 83.6, c = 88.3 {angstrom}, {beta} = 100.6{sup o}. The crystals diffracted to 2.39 {angstrom} resolution on a rotating-anode source. Based on the calculated Matthews coefficient (2.2 {angstrom}{sup 3} Da{sup -1}), it appears that the asymmetric unit contains four molecules.

  7. Crystallization and preliminary X-ray diffraction analysis of prephenate dehydratase from Mycobacterium tuberculosis H37Rv

    Energy Technology Data Exchange (ETDEWEB)

    Vivan, Ana Luiza [Programa de Pós Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil); Centro de Pesquisa em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Av. Ipiranga, 6681 Prédio 92A-TECNOPUC-Partenon, CEP 90619-900, Porto Alegre, RS (Brazil); Dias, Márcio Vinícius Bertacini [Programa de Pós Graduação em Biofísica Molecular, Departamento de Física, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000 (Brazil); Schneider, Cristopher Z. [Programa de Pós Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil); Centro de Pesquisa em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Av. Ipiranga, 6681 Prédio 92A-TECNOPUC-Partenon, CEP 90619-900, Porto Alegre, RS (Brazil); Azevedo, Walter Filgueira Jr de; Basso, Luiz Augusto, E-mail: luiz.basso@pucrs.br; Santos, Diógenes Santiago, E-mail: luiz.basso@pucrs.br [Centro de Pesquisa em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Av. Ipiranga, 6681 Prédio 92A-TECNOPUC-Partenon, CEP 90619-900, Porto Alegre, RS (Brazil); Programa de Pós Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil)

    2006-04-01

    The M. tuberculosis prephenate dehydratase was cloned, expressed, purified, crystallized by the hanging-drop vapour-diffusion method, and a complete data set collected to 3.2 Å resolution using synchrotron radiation. These results should pave the way for the three-dimensional structure determination of the enzyme and provide a framework on which to base the rational design of chemotherapeutic agents to treat tuberculosis. Tuberculosis remains the leading cause of mortality arising from a bacterial pathogen (Mycobacterium tuberculosis). There is an urgent need for the development of new antimycobacterial agents. The aromatic amino-acid pathway is essential for the survival of this pathogen and represents a target for structure-based drug design. Accordingly, the M. tuberculosis prephenate dehydratase has been cloned, expressed, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 400 as a precipitant. The crystal belongs to the orthorhombic space group I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 98.26, b = 133.22, c = 225.01 Å, and contains four molecules in the asymmetric unit. A complete data set was collected to 3.2 Å resolution using a synchrotron-radiation source.

  8. Crystallization and preliminary X-ray analysis of RsbS from Moorella thermoacetica at 2.5 A resolution.

    Science.gov (United States)

    Quin, Maureen; Newman, Joseph; Firbank, Susan; Lewis, Richard J; Marles-Wright, Jon

    2008-03-01

    The thermophilic bacterium Moorella thermoacetica possesses an rsb operon that is related to the genetic locus common to many Gram-positive bacteria that regulates the activity of the stress-responsive sigma factor sigma(B). One of the gene products of this operon is RsbS, a single STAS-domain protein that is a component of higher order assemblies in Bacillus subtilis known as 'stressosomes'. It is expected that similar complexes are found in M. thermoacetica, but in this instance regulating the biosynthesis of cyclic di-GMP, a ubiquitous secondary messenger. Selenomethionine-labelled MtRsbS protein was crystallized at room temperature using the hanging-drop vapour-diffusion method. Crystals belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.07, b = 60.52, c = 89.28 A, diffracted to 2.5 A resolution on beamline I04 of the Diamond Light Source. The selenium substructure was solved using SHELX and it is believed that this represents the first reported ab initio crystal structure to be solved using diffraction data collected at DLS.

  9. Expression, crystallization and preliminary X-ray diffraction analysis of human paired Ig-like type 2 receptor α (PILRα)

    Energy Technology Data Exchange (ETDEWEB)

    Tabata, Shigekazu; Kuroki, Kimiko; Maita, Nobuo [Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Wang, Jing; Shiratori, Ikuo [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 (Japan); Arase, Hisashi [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 (Japan); WPI Immunology Frontier Research Center, Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 (Japan); SORST, Japan Science and Technology Agency, Saitama 332-0012 (Japan); Kohda, Daisuke; Maenaka, Katsumi, E-mail: kmaenaka@bioreg.kyushu-u.ac.jp [Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)

    2008-01-01

    Human paired Ig-like type 2 receptor α (PILRα) has been expressed, purified and crystallized. A diffraction data set has been collected to 1.3 Å resolution. Human paired immunoglobulin-like (Ig-like) type 2 receptor α (PILRα) is a type I membrane protein that is mainly expressed in immune-related cells such as monocytes, granulocytes and dendritic cells. PILRα can suppress the functions of such immune cells because it has the immunoreceptor tyrosine-based inhibitory motif (ITIM) in the intracellular region, which recruits the phosphatase Src homology-2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP-2) to inhibit phophorylations induced by activation signals. The extracellular region of human PILRα comprises one immunoglobulin superfamily V-set domain and a stalk region. The V-set domain (residues 13–131) of human PILRα was overexpressed in Escherichia coli as inclusion bodies, refolded by rapid dilution and purified. The PILRα protein was successfully crystallized at 293 K using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.3 Å resolution at SPring-8 BL41XU; they belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 40.4, b = 45.0, c = 56.9 Å, and contain one molecule per asymmetric unit.

  10. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of variants of monoamine oxidase from Aspergillus niger

    Energy Technology Data Exchange (ETDEWEB)

    Atkin, Kate E. [Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Reiss, Renate; Turner, Nicholas J. [School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Brzozowski, Andrzej M.; Grogan, Gideon, E-mail: grogan@ysbl.york.ac.uk [Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW (United Kingdom)

    2008-03-01

    Crystals of A. niger monoamine oxidase variants display P2{sub 1} or P4{sub 1}2{sub 1}2/P4{sub 3}2{sub 1}2 symmetry, with eight or two molecules in the asymmetric unit, respectively. Monoamine oxidase from Aspergillus niger (MAO-N) is an FAD-dependent enzyme that catalyses the conversion of terminal amines to their corresponding aldehydes. Variants of MAO-N produced by directed evolution have been shown to possess altered substrate specificity. Crystals of two of these variants (MAO-N-3 and MAO-N-5) have been obtained; the former displays P2{sub 1} symmetry with eight molecules per asymmetric unit and the latter has P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2 symmetry and two molecules per asymmetric unit. Solution of these structures will help shed light on the molecular determinants of improved activity and high enantioselectivity towards a broad range of substrates.

  11. X-Ray Imaging Crystal Spectrometer for Extended X-Ray Sources

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, Manfred L.; Fraekel, Benjamin; Gorman, James L.; Hill, Kenneth W.; Roquemore, Lane A.; Stodiek, Wolfgang; Goeler, Schweickhard von

    1999-05-01

    Spherically or toroidally curved, double focusing crystals are used in a spectrometer for X-ray diagnostics of an extended X-ray source such as a hot plasma produced in a tokamak fusion experiment to provide spatially and temporally resolved data on plasma parameters such as ion temperature, toroidal and poloidal rotation, electron temperature, impurity ion charge-state distributions, and impurity transport. The imaging properties of these spherically or toroidally curved crystals provide both spectrally and spatially resolved X-ray data from the plasma using only one small spherically or toroidally curved crystal, thus eliminating the requirement for a large array of crystal spectrometers and the need to cross-calibrate the various crystals.

  12. Purification, crystallization and preliminary X-ray analysis of TP0435 (Tp17) from the syphilis spirochete Treponema pallidum.

    Science.gov (United States)

    Brautigam, Chad A; Deka, Ranjit K; Norgard, Michael V

    2013-04-01

    Syphilis, caused by the bacterial spirochete Treponema pallidum, remains a prominent sexually transmitted infection worldwide. Despite sequencing of the genome of this obligate human pathogen 15 years ago, the functions of a large number of the gene products of T. pallidum are still unknown, particularly with respect to those of the organism's periplasmic lipoproteins. To better understand their functions, a structural biology approach has been pursued. To this end, the soluble portion of the T. pallidum TP0435 lipoprotein (also known as Tp17) was cloned, hyper-expressed in Escherichia coli and purified to apparent homogeneity. The protein crystals obtained from this preparation diffracted to 2.4 Å resolution and had the symmetry of space group R3. In the hexagonal setting, the unit-cell parameters were a = b = 85.7, c = 85.4 Å.

  13. Purification, crystallization and preliminary X-ray diffraction analysis of the Staphylococcus epidermidis extracellular serine protease Esp.

    Science.gov (United States)

    Vengadesan, Krishnan; Macon, Kevin; Sugumoto, Shinya; Mizunoe, Yoshimitsu; Iwase, Tadayuki; Narayana, Sthanam V L

    2013-01-01

    Esp, an extracellular serine protease from Staphylococcus epidermidis, has been shown to inhibit S. aureus biofilm formation and nasal colonization. The full-length 27 kDa pro-Esp was purified and digested with thermolysin to obtain mature Esp. The mature Esp containing 216 residues crystallized in space group P2(1), with unit-cell parameters a = 39.5, b = 61.2, c = 42.5 Å, β = 98.2° and one molecule in the asymmetric unit, with an estimated solvent content of 42%. A diffraction data set has been collected to 1.8 Å resolution on a rotating-anode home-source facility.

  14. Crystallization and preliminary X-ray studies of dUTPase from Mason–Pfizer monkey retrovirus

    Energy Technology Data Exchange (ETDEWEB)

    Barabás, Orsolya; Németh, Veronika; Vértessy, Beáta G., E-mail: vertessy@enzim.hu [Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Karolina út 29, H-1113 (Hungary)

    2006-04-01

    Deoxyuridine 5′-triphosphate nucleotidohydrolase from Mason–Pfizer monkey retrovirus (M-PMV dUTPase) is a betaretroviral member of the dUTPase enzyme family. The nucleocapsid-free dUTPase (48426 Da) was co-crystallized with a dUTP substrate analogue using the hanging-drop vapour-diffusion method. Deoxyuridine 5′-triphosphate nucleotidohydrolase from Mason–Pfizer monkey retrovirus (M-PMV dUTPase) is a betaretroviral member of the dUTPase enzyme family. In the mature M-PMV virion, this enzyme is present as the C-terminal domain of the fusion protein nucleocapsid-dUTPase. The homotrimeric organization characteristic of dUTPases is retained in this bifunctional fusion protein. The fusion protein supposedly plays a role in adequate localization of dUTPase activity in the vicinity of nucleic acids during reverse transcription and integration. Here, the nucleocapsid-free dUTPase (48 426 Da) was cocrystallized with a dUTP substrate analogue using the hanging-drop vapour-diffusion method. The obtained crystals belong to the primitive hexagonal space group P6{sub 3}, with unit-cell parameters a = 60.6, b = 60.6, c = 63.6 Å, α = 90, β = 90, γ = 120°. Native and PtCl{sub 4}-derivative data sets were collected using synchrotron radiation to 1.75 and 2.3 Å, respectively. Phasing was successfully performed by isomorphous replacement combined with anomalous scattering.

  15. X-ray optics the diffraction of X-rays by finite and imperfect crystals

    CERN Document Server

    Wilson, Arthur J C

    1949-01-01

    This fascinating text contains a detailed treatise on the use of X-Ray optics in the taxonomy of minerals and gem stones. An interesting and informative book on the subject, X-Ray Optics - The Diffraction of X-Rays by Finite and Imperfect Crystals is a must-have for anyone with an interest the study of crystals and constitutes a great addition to any gemmological collection. Arthur James Cochran Wilson (28 November 1914 - 1 July 1995) was a Canadian crystallographer, most famous for his contributions to X-ray crystallography and elected as a Fellow of the Royal Society in 1963. This book has been elected for republication now due to its immense educational value, and is proudly republished here complete with a new introduction to the subject.

  16. Crystallization and preliminary X-ray crystallographic study on a xyloglucan-specific exo-beta-glycosidase, oligoxyloglucan reducing-end specific cellobiohydrolase.

    Science.gov (United States)

    Yaoi, Katsuro; Kondo, Hidemasa; Suzuki, Mamoru; Noro, Natsuko; Tsuda, Sakae; Mitsuishi, Yasushi

    2003-10-01

    A novel xyloglucan-specific exo-beta-glycosidase, oligoxyloglucan reducing-end specific cellobiohydrolase (OXG-RCBH), recognizes the reducing end of oligoxyloglucan and releases two glucosyl residue segments from the main chain. OXG-RCBH was crystallized by the hanging-drop vapour-diffusion method with polyethylene glycol 3000 and polyethylene glycol 400 as precipitants. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 61.0, b = 146.9, c = 211.9 A. The crystals diffract to a resolution of 2.2 A and are suitable for X-ray structure analysis.

  17. Crystallization, Preliminary X-ray Diffraction and Structure Solution of MosA, a Dihydrodipicolinate Synthase from Sinorhizobium Meliloti L5-30

    Energy Technology Data Exchange (ETDEWEB)

    Leduc,Y.; Phenix, C.; Puttick, J.; Nienaber, K.; Palmer, D.; Delbaere, L.

    2006-01-01

    The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Angstroms resolution using synchrotron radiation and belonged to the orthorhombic space group C2221, with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Angstroms.

  18. High-resolution x-ray characterization of mosaic crystals for hard x-ray astronomy

    Science.gov (United States)

    Ferrari, Claudio; Buffagni, Elisa; Marchini, Laura; Zappettini, Andrea

    2012-04-01

    GaAs, Cu, CdTe, and CdZnTe crystals have been studied as optical elements for lenses for hard x-ray astronomy. High-resolution x-ray diffraction at 8 keV in Bragg geometry and at synchrotron at energies up to 500 keV in Laue geometry has been used. A good agreement was found between the mosaicity evaluated in Bragg geometry at 8 keV with x-ray penetration of the order of few tens of micrometers and that derived at synchrotron in transmission Laue geometry at higher x-ray energies. Mosaicity values in a range between a few to 150 arcsec were found in all the samples but, due to the presence of crystal grains in the cm range, CdTe and CdZnTe crystals were found not suitable. Cu crystals exhibit a mosaicity of the order of several arcmin; they indeed were found to be severely affected by cutting damage which could only be removed with a very deep etching. The full width at half maximum of the diffraction peaks decreased at higher x-ray energies showing that the peak broadening is affected by crystallite size. GaAs crystals grown by Czochralski method showed a mosaic spread up to 30 arcsec and good diffraction efficiency up to energies of 500 keV. The use of thermal treatments as a possible method to increase the mosaic spread was also evaluated.

  19. Crystallization and preliminary X-ray crystallographic studies of a Lys49-phospholipase A2 homologue from Bothrops pirajai venom complexed with rosmarinic acid

    Science.gov (United States)

    dos Santos, Juliana I.; Santos-Filho, Norival A.; Soares, Andreimar M.; Fontes, Marcos R. M.

    2010-01-01

    PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A2 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 P212121, indicating conformational changes in the structure after ligand binding: the crystals of all apo Lys49-phospholipase A2 structures belong to space group P3121, while the crystals of complexed structures belong to space groups P21 or P212121. PMID:20516603

  20. Expression, purification, crystallization and preliminary X-ray analysis of the native class C beta-lactamase from Enterobacter cloacae 908R and two mutants.

    Science.gov (United States)

    Wouters, J; Charlier, P; Monnaie, D; Frère, J M; Fonzé, E

    2001-01-01

    Crystals have been obtained of the Enterobacter cloacae 908R beta-lactamase and two point mutants by the vapour-diffusion method using similar conditions [pH 9.0, polyethylene glycol (M(r) = 6000) as precipitant]. The three crystal forms belong to the orthorhombic space group P2(1)2(1)2, with roughly the same unit-cell parameters; i.e. for the wild-type crystals a = 46.46, b = 82.96, c = 95.31 A. In the best cases, the crystals diffract to about 2.1 A resolution on a rotating-anode X-ray source at room temperature. Co-crystallization experiments of poor substrates with the wild-type protein and the active-site serine mutant (S64C) are planned and should lead to a better understanding of the catalytic mechanism of class C beta-lactamases.

  1. Crystallization, optimization and preliminary X-ray characterization of a metal-dependent PI-PLC from Streptomyces antibioticus

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Michael R.; Selby, Thomas L.

    2012-10-30

    A recombinant metal-dependent phosphatidylinositol-specific phospholipase C (PI-PLC) fromStreptomyces antibioticushas been crystallized by the hanging-drop method with and without heavy metals. The native crystals belonged to the orthorhombic space groupP222, with unit-cell parametersa= 41.26,b= 51.86,c = 154.78 Å. The X-ray diffraction results showed significant differences in the crystal quality of samples soaked with heavy atoms. Additionally, drop pinning, which increases the surface area of the drops, was also used to improve crystal growth and quality. The combination of heavy-metal soaks and drop pinning was found to be critical for producing high-quality crystals that diffracted to 1.23 Å resolution.

  2. Crystallization and preliminary X-ray diffraction study of recombinant adenine phosphoribosyltransferase from the thermophilic bacterium Thermus thermophilus strain HB27

    Science.gov (United States)

    Sinitsyna, E. V.; Timofeev, V. I.; Tuzova, E. S.; Kostromina, M. A.; Murav'eva, T. I.; Esipov, R. S.; Kuranova, I. P.

    2017-07-01

    Adenine phosphoribosyltransferase (APRT) belongs to the type I phosphoribosyltransferase family and catalyzes the formation of adenosine monophosphate via transfer of the 5-phosphoribosyl group from phosphoribosyl pyrophosphate to the nitrogen atom N9 of the adenine base. Proteins of this family are involved in a salvage pathway of nucleotide synthesis, thus providing purine base utilization and maintaining the optimal level of purine bases in the body. Adenine phosphoribosyltransferase from the extremely thermophilic Thermus thermophilus strain HB27 was produced using a highly efficient E. coli producer strain and was then purified by affinity and gel-filtration chromatography. This enzyme was successfully employed as a catalyst for the cascade biosynthesis of biologically important nucleotides. The screening of crystallization conditions for recombinant APRT from T. thermophilus HB27 was performed in order to determine the enzyme structure by X-ray diffraction. The crystallization conditions, which were found by the vapor-diffusion technique, were then optimized to apply the counter-diffusion technique. The crystals of the enzyme were grown by the capillary counter-diffusion method. The crystals belong to sp. gr. P1211 and have the following unitcell parameters: a = 69.86 Å, b = 82.16 Å, c = 91.39 Å, α = γ = 90°, β = 102.58°. The X-ray diffraction data set suitable for the determination of the APRT structure at 2.6 Å resolution was collected from the crystals at the SPring-8 synchrotron facility (Japan).

  3. Stig Sundell at the bent crystal X-ray spectrometer for the X-ray shift experiment.

    CERN Multimedia

    CERN PhotoLab

    1976-01-01

    The bent crystal X-ray spectrometer is being used to measure small shifts in the frequencies of X-rays emitted from the lower electron energy levels, in order to learn about the size of the nuclei concerned

  4. Crystallization and preliminary X-ray crystallographic analysis of the tetracycline-degrading monooxygenase TetX2 from Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Volkers, Gesa; Schuldt, Linda; Palm, Gottfried J; Wright, Gerard D; Hinrichs, Winfried

    2010-05-01

    The flavin-dependent monooxygenase TetX2 from Bacteroides thetaiotaomicron confers resistance against tetracyclines in aerobically grown Escherichia coli. TetX2 modifies several tetracycline antibiotics by regioselective hydroxylation of the substrates to 11a-hydroxy-tetracyclines. X-ray diffraction data were collected from a native TetX2 crystal and a TetX2 crystal with incorporated selenomethionine to resolutions of 2.5 and 3.0 A, respectively. The native crystal belonged to the triclinic space group P1, with unit-cell parameters a = 68.55, b = 80.88, c = 87.53 A, alpha = 111.09, beta = 98.98, gamma = 93.38 degrees , whereas the selenomethionine-labelled TetX2 crystal belonged to the monoclinic space group P2(1), with unit-cell parameters a = 87.34, b = 68.66, c = 152.48 A, beta = 101.08 degrees .

  5. Expression, purification, crystallization, and preliminary X-ray crystallographic analysis of OXA-17, an extended-spectrum {beta}-lactamase conferring severe antibiotic resistance

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H., E-mail: msgjhlee@mju.ac.kr; Sohn, S. G., E-mail: sgsohn@mju.ac.kr; Jung, H. I., E-mail: jhinumber1@hanmail.net; An, Y. J., E-mail: anyj0120@hanmail.net; Lee, S. H., E-mail: sangheelee@mju.ac.kr [Myongji University, Drug Resistance Proteomics Laboratory, Department of Biological Sciences (Korea, Republic of)

    2013-07-15

    OXA-17, an extended-spectrum {beta}-lactamase (ESBL) conferring severe antibiotic resistance, hydrolytically inactivates {beta}-lactam antibiotics, inducing a lack of eradication of pathogenic bacteria by oxyimino {beta}-lactams and not helping hospital infection control. Thus, the enzyme is a potential target for developing antimicrobial agents against pathogens producing ESBLs. OXA-17 was purified and crystallized at 298 K. X-ray diffraction data from OXA-17 crystal have been collected to 1.85 A resolution using synchrotron radiation. The crystal of OXA-17 belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 48.37, b = 101.12, and c = 126.07 A. Analysis of the packing density shows that the asymmetric unit probably contains two molecules with a solvent content of 54.6%.

  6. Purification, crystallization, and preliminary X-ray analysis of PepX, an X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis.

    Science.gov (United States)

    Chich, J F; Rigolet, P; Nardi, M; Gripon, J C; Ribadeau-Dumas, B; Brunie, S

    1995-10-01

    The X-prolyl dipeptidyl aminopeptidase PepX, a serine peptidase isolated originally from Lactococcus lactis subsp lactis NCDO 763, was cloned and overproduced in Escherichia coli. The enzyme was isolated in its active form in two purification steps. Crystals of PepX were grown by the hanging drop vapor diffusion method using polyethyleneglycol 4000 as precipitant at pH 5.0. The crystals are orthorhombic with cell dimensions a = 92.8 A, b = 102.6 A, and c = 101.6 A, space group P2(1)2(1)2, and probably contain one monomer of 87.5 kDa in the asymmetric unit. The crystals, very stable under X-rays, diffract to at least 2.2 A and are suitable for high-resolution structural analysis.

  7. Purification, crystallization and preliminary X-ray diffraction analysis of RafE, a sugar-binding lipoprotein from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    Paterson, Neil G., E-mail: neison@chem.gla.ac.uk; Riboldi-Tunnicliffe, Alan [Department of Chemistry and WestCHEM, Glasgow Biomedical Research Centre (GBRC), University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom); Mitchell, Timothy J. [Division of Infection and Immunity (IBLS), Glasgow Biomedical Research Centre (GBRC), University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom); Isaacs, Neil W. [Department of Chemistry and WestCHEM, Glasgow Biomedical Research Centre (GBRC), University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom)

    2006-07-01

    The mature form of RafE has been expressed, purified and crystallized. X-ray diffraction data have been collected to 3.65 and 2.90 Å resolution from native and selenomethionine-derivative crystals, respectively. Streptococcus pneumoniae contains a large number of sugar-transport systems and the system responsible for raffinose uptake has recently been identified. The substrate-binding protein component of this system shares strong sequence homology with the multiple sugar metabolism substrate-binding protein MsmE from S. mutans and contains a lipoprotein-attachment site at cysteine residue 23. A truncated form (residues 24–419) of RafE from S. pneumoniae was cloned and overexpressed in Escherichia coli. Native and selenomethionine-labelled protein have been crystallized in the hexagonal space group P6{sub 1}22. Diffraction data have been successfully phased to 2.90 Å using Se SAD data and model building is in progress.

  8. The complex between SOS3 and SOS2 regulatory domain from Arabidopsis thaliana: cloning, expression, purification, crystallization and preliminary X-ray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Barrena, María José; Moreno-Pérez, Sandra; Angulo, Iván; Martínez-Ripoll, Martín; Albert, Armando, E-mail: xalbert@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid (Spain)

    2007-07-01

    Recombinant SOS3 and SOS2 regulatory domain from A. thaliana have been coexpressed in E. coli, purified and crystallized by the hanging-drop vapour-diffusion method. An X-ray data set has been collected at 2.0 Å resolution. The salt-tolerance genes SOS3 (salt overly sensitive 3) and SOS2 (salt overly sensitive 2) regulatory domain of Arabidopsis thaliana were cloned into a polycistronic plasmid and the protein complex was expressed in Escherichia coli, allowing purification to homogeneity in three chromatographic steps. Crystals were grown using vapour-diffusion techniques. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 44.14, b = 57.39, c = 141.90 Å.

  9. Crystallization and preliminary X-ray diffraction analysis of a novel Arg49 phospholipase A{sub 2} homologue from Zhaoermia mangshanensis venom

    Energy Technology Data Exchange (ETDEWEB)

    Murakami, Mário T. [Department of Physics, UNESP-State University of São Paulo, São José do Rio Preto 15054-000 (Brazil); Center for Applied Toxinology, CAT-CEPID, São Paulo, SP (Brazil); Advanced Center for Genomics and Proteomics, UNESP-State University of São Paulo, São José do Rio Preto 15054-000 (Brazil); Kuch, Ulrich; Mebs, Dietrich [Zentrum der Rechtsmedizin, Klinikum der Johann Wolfgang Goethe-Universität, Kennedyallee 104, D-60596 Frankfurt am Main (Germany); Arni, Raghuvir K., E-mail: arni@ibilce.unesp.br [Department of Physics, UNESP-State University of São Paulo, São José do Rio Preto 15054-000 (Brazil); Center for Applied Toxinology, CAT-CEPID, São Paulo, SP (Brazil); Advanced Center for Genomics and Proteomics, UNESP-State University of São Paulo, São José do Rio Preto 15054-000 (Brazil)

    2007-07-01

    A single crystal of zhaoermiatoxin with maximum dimensions of 0.2 × 0.2 × 0.5 mm was used for X-ray diffraction data collection to a resolution of 2.05 Å using synchrotron radiation and the diffraction pattern was indexed in the hexagonal space group P6{sub 4}, with unit-cell parameters a = 72.9, b = 72.9, c = 93.9 Å. Zhaoermiatoxin, an Arg49 phospholipase A{sub 2} homologue from Zhaoermia mangshanensis (formerly Trimeresurus mangshanensis, Ermia mangshanensis) venom is a novel member of the PLA{sub 2}-homologue family that possesses an arginine residue at position 49, probably arising from a secondary Lys49→Arg substitution that does not alter the catalytic inactivity towards phospholipids. Like other Lys49 PLA{sub 2} homologues, zhaoermiatoxin induces oedema and strong myonecrosis without detectable PLA{sub 2} catalytic activity. A single crystal with maximum dimensions of 0.2 × 0.2 × 0.5 mm was used for X-ray diffraction data collection to a resolution of 2.05 Å using synchrotron radiation and the diffraction pattern was indexed in the hexagonal space group P6{sub 4}, with unit-cell parameters a = 72.9, b = 72.9, c = 93.9 Å.

  10. Crystallization, preliminary X-ray diffraction and structure solution of MosA, a dihydrodipicolinate synthase from Sinorhizobium meliloti L5-30

    Energy Technology Data Exchange (ETDEWEB)

    Leduc, Yvonne A. [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada); Phenix, Christopher P. [Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9 (Canada); Puttick, Jennifer; Nienaber, Kurt [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada); Palmer, David R. J. [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada); Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9 (Canada); Delbaere, Louis T. J., E-mail: louis.delbaere@usask.ca [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada)

    2006-01-01

    MosA from S. meliloti L5-30 has been crystallized in solution with pyruvate and the 2.3 Å resolution structure has been solved by molecular replacement using E. coli dihydrodipicolinate synthase as the model. The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Å resolution using synchrotron radiation and belonged to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Å.

  11. Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta).

    Science.gov (United States)

    McCarthy, Andrew A; Biget, Laurent; Lin, Chenwei; Petiard, Vincent; Tanksley, Steve D; McCarthy, James G

    2007-04-01

    Caffeine is a secondary metabolite produced by a variety of plants including Coffea canephora (robusta) and there is growing evidence that caffeine is part of a chemical defence strategy protecting young leaves and seeds from potential predators. The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-L-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). The crystals are orthorhombic, with space group P2(1)2(1)2(1) for XMT and C222(1) for DXMT. X-ray diffraction to 2.8 A for XMT and to 2.5 A for DXMT have been collected on beamline ID23-1 at the ESRF.

  12. Purification, crystallization and preliminary X-ray diffraction analysis of GatD, a glutamine amidotransferase-like protein from Staphylococcus aureus peptidoglycan.

    Science.gov (United States)

    Vieira, Diana; Figueiredo, Teresa A; Verma, Anil; Sobral, Rita G; Ludovice, Ana M; de Lencastre, Hermínia; Trincao, Jose

    2014-05-01

    Amidation of peptidoglycan is an essential feature in Staphylococcus aureus that is necessary for resistance to β-lactams and lysozyme. GatD, a 27 kDa type I glutamine amidotransferase-like protein, together with MurT ligase, catalyses the amidation reaction of the glutamic acid residues of the peptidoglycan of S. aureus. The native and the selenomethionine-derivative proteins were crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol, sodium acetate and calcium acetate. The crystals obtained diffracted beyond 1.85 and 2.25 Å, respectively, and belonged to space group P212121. X-ray diffraction data sets were collected at Diamond Light Source (on beamlines I02 and I04) and were used to obtain initial phases.

  13. Crystallization and preliminary X-ray analysis of Salmonella FliI, the ATPase component of the type III flagellar protein-export apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Minamino, Tohru; Imada, Katsumi, E-mail: kimada@fbs.osaka-u.ac.jp [Dynamic NanoMachine Project, ICORP, JST, 1-3 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 (Japan); Tahara, Aiko [Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kihara, May; Macnab, Robert M. [Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114 (United States); Namba, Keiichi [Dynamic NanoMachine Project, ICORP, JST, 1-3 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2006-10-01

    Crystals of an N-terminally truncated variant of the Salmonella flagellar ATPase FliI, which exports substrate proteins into the central channel of the growing flagellar structure by utilizing the energy of ATP hydrolysis, have been obtained and characterized by X-ray diffraction. Most of the structural components making up the bacterial flagellum are translocated through the central channel of the growing flagellar structure by the type III flagellar protein-export apparatus in an ATPase-driven manner and are assembled at the growing end. FliI is the ATPase that drives flagellar protein export using the energy of ATP hydrolysis. FliI forms an oligomeric ring structure in order to attain maximum ATPase activity. In this study, FliI(Δ1–18), an N-terminally truncated variant of FliI lacking the first 18 residues, was purified and crystallized. Crystals were obtained using the hanging-drop vapour-diffusion technique with PEG 8000 as a precipitant. FliI(Δ1–18) crystals grew in the monoclinic space group P2{sub 1}, with unit-cell parameters a = 48, b = 73, c = 126 Å, β = 94°, and diffracted to 2.4 Å resolution. Anomalous difference Patterson maps of Os-derivative and Pt-derivative crystals showed significant peaks in their Harker sections, indicating that both derivatives are suitable for structure determination.

  14. Expression, purification, crystallization and preliminary X-ray characterization of a putative glycosyltransferase of the GT-A fold found in mycobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Fulton, Zara [The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800 (Australia); Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800 (Australia); Crellin, Paul K.; Brammananth, Rajini [Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800 (Australia); Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800 (Australia); Zaker-Tabrizi, Leyla [The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800 (Australia); Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800 (Australia); Coppel, Ross L. [Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800 (Australia); Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800 (Australia); Rossjohn, Jamie, E-mail: jamie.rossjohn@med.monash.edu.au; Beddoe, Travis, 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); Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800 (Australia)

    2008-05-01

    MAP2569c from M. avium subsp. paratuberculosis, a putative glycosyltransferase implicated in mycobacterial cell-wall biosynthesis, was cloned, expressed, purified and crystallized. X-ray diffraction data were collected to 1.8 Å resolution. Glycosidic bond formation is a ubiquitous enzyme-catalysed reaction. This glycosyltransferase-mediated process is responsible for the biosynthesis of innumerable oligosaccharides and glycoconjugates and is often organism- or cell-specific. However, despite the abundance of genomic information on glycosyltransferases (GTs), there is a lack of structural data for this versatile class of enzymes. Here, the cloning, expression, purification and crystallization of an essential 329-amino-acid (34.8 kDa) putative GT of the classic GT-A fold implicated in mycobacterial cell-wall biosynthesis are reported. Crystals of MAP2569c from Mycobacterium avium subsp. paratuberculosis were grown in 1.6 M monoammonium dihydrogen phosphate and 0.1 M sodium citrate pH 5.5. A complete data set was collected to 1.8 Å resolution using synchrotron radiation from a crystal belonging to space group P4{sub 1}2{sub 1}2.

  15. Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jun Hyuck; Park, Soo Jeong; Rho, Seong-Hwan; Im, Young Jun; Kim, Mun-Kyoung; Kang, Gil Bu; Eom, Soo Hyun, E-mail: eom@gist.ac.kr [Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of)

    2005-11-01

    The GluR0 ligand-binding core from N. punctiforme was expressed, purified and crystallized in the presence of l-glutamate. A diffraction data set was collected to a resolution of 2.1 Å. GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The l-glutamate-complexed crystal belongs to space group C222{sub 1}, with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 Å. The crystals contain three subunits in the asymmetric unit, with a V{sub M} value of 2.49 Å{sup 3} Da{sup −1}. The diffraction limit of the l-glutamate complex data set was 2.1 Å using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea)

  16. Crystallization and preliminary X-ray diffraction analysis of the carbohydrate-recognizing domain (VP8*) of bovine rotavirus strain NCDV.

    Science.gov (United States)

    Yu, Xing; Guillon, Annabel; Szyczew, Alex J; Kiefel, Milton J; Coulson, Barbara S; von Itzstein, Mark; Blanchard, Helen

    2008-06-01

    The infectivity of rotavirus is dramatically enhanced by proteolytic cleavage of its outer layer VP4 spike protein into two functional domains, VP8* and VP5*. The carbohydrate-recognizing domain VP8* is proposed to bind sialic acid-containing host cell-surface glycans and this is followed by a series of subsequent virus-cell interactions. Live attenuated human and bovine rotavirus vaccine candidates for the prevention of gastroenteritis have been derived from bovine rotavirus strain NCDV. The NCDV VP8*(64-224) was overexpressed, purified to homogeneity and crystallized in the presence of an N-acetylneuraminic acid derivative. X-ray diffraction data were collected to a resolution of 2.0 A and the crystallographic structure of NCDV VP8*(64-224) was determined by molecular replacement.

  17. X-ray scattering from surfaces of organic crystals

    DEFF Research Database (Denmark)

    Gidalevitz, D.; Feidenhans'l, R.; Smilgies, D.-M.

    1997-01-01

    X-ray scattering experiments have been performed on the surfaces of organic crystals. The (010) cleavage planes of beta-alanine and alpha-glycine were investigated, and both specular and off-specular crystal truncation rods were measured. This allowed a determination of the molecular layering...

  18. X-Ray structural investigation of VAS-393 crystals

    CERN Document Server

    Martirosian, A H; Harurtjunian, V S

    2001-01-01

    X-ray structural study of VAS-393 crystals was performed. Investigations were carried out with the use of the Weissenberg rotating and powder (employing the Bjornstrem diagrams) methods. The lattice constants ''c'' and ''a''are calculated. The crystal is shown to belong to the trigonal syngony (medium category)

  19. Purification, partial characterization, crystallization and preliminary X-ray diffraction of a novel cardiotoxin-like basic protein from Naja naja atra (South Anhui) venom

    Energy Technology Data Exchange (ETDEWEB)

    Rong, Hui; Li, Yan; Lou, Xiao-hua; Zhang, Xio; Gao, Yong-xiang; Teng, Mai-kun, E-mail: mkteng@ustc.edu.cn; Niu, Li-wen, E-mail: mkteng@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China)

    2007-02-01

    A novel cardiotoxin-like basic protein from Naja naja atra was crystallized and diffraction data were collected to 2.35 Å resolution. A novel cardiotoxin-like basic protein was isolated from the venom of the Chinese cobra (Naja naja atra) from the south of Anhui in China. The protein inhibits the expression of vascular endothelial growth factor and basic fibroblast growth factor in human lung cancer cell line H1299 and induces the haemolysis of rabbit erythrocytes under low-lecithin conditions. After a two-step chromatographic purification, the resultant 7 kDa protein was crystallized by the hanging-drop vapour-diffusion method at room temperature. A complete data set was collected to 2.35 Å resolution using an in-house X-ray diffraction system. The crystal belongs to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 43.2, c = 147.9 Å. There are two molecules in the crystallographic asymmetric unit.

  20. Purification, crystallization and preliminary X-ray diffraction analysis of a hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) from Coffea canephora involved in chlorogenic acid biosynthesis.

    Science.gov (United States)

    Lallemand, Laura A; McCarthy, James G; McSweeney, Sean; McCarthy, Andrew A

    2012-07-01

    Chlorogenic acids (CGAs) are a group of soluble phenolic compounds that are produced by a variety of plants, including Coffea canephora (robusta coffee). The last step in CGA biosynthesis is generally catalysed by a specific hydroxycinnamoyl-CoA quinate hydroxycinnamoyltransferase (HQT), but it can also be catalysed by the more widely distributed hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT). Here, the cloning and overexpression of HCT from C. canephora in Escherichia coli as well as its purification and crystallization are presented. Crystals were obtained by the sitting-drop technique at 293 K and X-ray diffraction data were collected on the microfocus beamline ID23-2 at the ESRF. The HCT crystals diffracted to better than 3.0 Å resolution, belonged to space group P4(2)2(1)2 with unit-cell parameters a = b = 116.1, c = 158.9 Å and contained two molecules in the asymmetric unit. The structure was solved by molecular replacement and is currently under refinement. Such structural data are needed to decipher the molecular basis of the substrate specifities of this key enzyme, which belongs to the large plant acyl-CoA-dependent BAHD acyltransferase superfamily.

  1. Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, Andrew A., E-mail: andrewmc@embl.fr [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France); Biget, Laurent [Nestlé Research and Development, 101 Avenue Gustave Eiffel, Notre-Dame D’Oe, 37097 Tours (France); Lin, Chenwei [Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853 (United States); Petiard, Vincent [Nestlé Research and Development, 101 Avenue Gustave Eiffel, Notre-Dame D’Oe, 37097 Tours (France); Tanksley, Steve D. [Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853 (United States); McCarthy, James G. [Nestlé Research and Development, 101 Avenue Gustave Eiffel, Notre-Dame D’Oe, 37097 Tours (France); European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France)

    2007-04-01

    The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-l-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). Caffeine is a secondary metabolite produced by a variety of plants including Coffea canephora (robusta) and there is growing evidence that caffeine is part of a chemical defence strategy protecting young leaves and seeds from potential predators. The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-l-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). The crystals are orthorhombic, with space group P2{sub 1}2{sub 1}2{sub 1} for XMT and C222{sub 1} for DXMT. X-ray diffraction to 2.8 Å for XMT and to 2.5 Å for DXMT have been collected on beamline ID23-1 at the ESRF.

  2. Preliminary small-angle X-ray scattering and X-ray diffraction studies of the BTB domain of lola protein from Drosophila melanogaster

    Science.gov (United States)

    Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Dorovatovskii, P. V.; Popov, V. O.

    2017-11-01

    The Drosophila genome has several dozens of transcription factors (TTK group) containing BTB domains assembled into octamers. The LOLA protein belongs to this family. The purification, crystallization, and preliminary X-ray diffraction and small-angle X-ray scattering (SAXS) studies of the BTB domain of this protein are reported. The crystallization conditions were found by the vapor-diffusion technique. A very low diffraction resolution (8.7 Å resolution) of the crystals was insufficient for the determination of the threedimensional structure of the BTB domain. The SAXS study demonstrated that the BTB domain of the LOLA protein exists as an octamer in solution.

  3. A short working distance multiple crystal x-ray spectrometer

    Science.gov (United States)

    Dickinson, B.; Seidler, G.T.; Webb, Z.W.; Bradley, J.A.; Nagle, K.P.; Heald, S.M.; Gordon, R.A.; Chou, I.-Ming

    2008-01-01

    For x-ray spot sizes of a few tens of microns or smaller, a millimeter-sized flat analyzer crystal placed ???1 cm from the sample will exhibit high energy resolution while subtending a collection solid angle comparable to that of a typical spherically bent crystal analyzer (SBCA) at much larger working distances. Based on this observation and a nonfocusing geometry for the analyzer optic, we have constructed and tested a short working distance (SWD) multicrystal x-ray spectrometer. This prototype instrument has a maximum effective collection solid angle of 0.14 sr, comparable to that of 17 SBCA at 1 m working distance. We find good agreement with prior work for measurements of the Mn K?? x-ray emission and resonant inelastic x-ray scattering for MnO, and also for measurements of the x-ray absorption near-edge structure for Dy metal using L??2 partial-fluorescence yield detection. We discuss future applications at third- and fourth-generation light sources. For concentrated samples, the extremely large collection angle of SWD spectrometers will permit collection of high-resolution x-ray emission spectra with a single pulse of the Linac Coherent Light Source. The range of applications of SWD spectrometers and traditional multi-SBCA instruments has some overlap, but also is significantly complementary. ?? 2008 American Institute of Physics.

  4. Purification, crystallization and preliminary X-ray diffraction analysis of the IL-20-IL-20R1-IL-20R2 complex

    Energy Technology Data Exchange (ETDEWEB)

    Logsdon, Naomi J.; Allen, Christopher E.; Rajashankar, Kanagalaghatta R.; Walter, Mark R. (Cornell); (UAB)

    2012-02-08

    Interleukin-20 (IL-20) is an IL-10-family cytokine that regulates innate and adaptive immunity in skin and other tissues. In addition to protecting the host from various external pathogens, dysregulated IL-20 signaling has been shown to contribute to the pathogenesis of human psoriasis. IL-20 signals through two cell-surface receptor heterodimers, IL-20R1-IL-20R2 and IL-22R1-IL-20R2. In this report, crystals of the IL-20-IL-20R1-IL-20R2 ternary complex have been grown from polyethylene glycol solutions. The crystals belonged to space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = 111, c = 135 {angstrom}, and diffracted X-rays to 3 {angstrom} resolution. The crystallographic asymmetric unit contains one IL-20-IL-20R1-IL-20R2 complex, corresponding to a solvent content of approximately 54%.

  5. Purification, crystallization and preliminary X-ray diffraction analysis of inner membrane complex (IMC) subcompartment protein 1 (ISP1) from Toxoplasma gondii.

    Science.gov (United States)

    Tonkin, Michelle L; Brown, Shannon; Beck, Josh R; Bradley, Peter J; Boulanger, Martin J

    2012-07-01

    The protozoan parasites of the Apicomplexa phylum are devastating global pathogens. Their success is largely due to phylum-specific proteins found in specialized organelles and cellular structures. The inner membrane complex (IMC) is a unique apicomplexan structure that is essential for motility, invasion and replication. The IMC subcompartment proteins (ISP) have recently been identified in Toxoplasma gondii and shown to be critical for replication, although their specific mechanisms are unknown. Structural characterization of TgISP1 was pursued in order to identify the fold adopted by the ISPs and to generate detailed insight into how this family of proteins functions during replication. An N-terminally truncated form of TgISP1 was purified from Escherichia coli, crystallized and subjected to X-ray diffraction analysis. Two crystal forms of TgISP1 belonging to space groups P4(1)32 or P4(3)32 and P2(1)2(1)2(1) diffracted to 2.05 and 2.1 Å resolution, respectively.

  6. Crystallization and preliminary X-ray diffraction study of the class A beta-lactamase SED-1 and its mutant SED-G238C from Citrobacter sedlakii.

    Science.gov (United States)

    Petrella, S; Pernot, L; Sougakoff, W

    2004-01-01

    SED-1, a class A beta-lactamase from Citrobacter sedlakii, is a CTX-M-type extended-spectrum beta-lactamase that has the ability to hydrolyze expanded-spectrum cephalosporins such as cefotaxime. SED-1 and a SED mutant in which Gly238 has been replaced by a cysteine, forming a disulfide bridge with the other Cys residue located at position 69 (SED-G238C), have been crystallized. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 188.09, b = 73.65, c = 105.41 A, beta = 121.67 degrees for SED-1 and a = 187.64, b = 73.2, c = 103.89 A, beta = 121.89 degrees for the SED-G238C mutant. X-ray diffraction data were collected to maximum resolutions of 2.4 A for SED-1 and 2.0 A for SED-G238C.

  7. Crystallization and preliminary X-ray analysis of BigR, a transcription repressor from Xylella fastidiosa involved in biofilm formation

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, Rosicler Lázaro; Rinaldi, Fábio Cupri; Guimarães, Beatriz Gomes, E-mail: beatriz@lnls.br; Benedetti, Celso Eduardo, E-mail: beatriz@lnls.br [Center for Molecular and Structural Biology, Brazilian Synchrotron Light Laboratory, Campinas, SP, CP 6192, CEP 13083-970 (Brazil)

    2007-07-01

    In order to gain new insights into the protein structure and its possible interaction with a metal ion or effector ligand, BigR from X. fastidiosa was crystallized in native and selenomethionine (SeMet) labelled forms using the hanging-drop vapour-diffusion method. BigR (biofilm growth-associated repressor) is a novel repressor protein that regulates the transcription of an operon implicated in biofilm growth in both Xylella fastidiosa and Agrobacterium tumefaciens. This protein binds to a palindromic TA-rich element located in the promoter of the BigR operon and strongly represses transcription of the operon. BigR contains a helix–turn–helix (HTH) domain that is found in some members of the ArsR/SmtB family of metal sensors, which control metal resistance in bacteria. Although functional studies have suggested that BigR does not act as a metal sensor, the presence of two cysteines and a methionine in its primary structure raised the possibility of BigR being a metal-ligand protein. In order to gain new insights into the protein structure and its possible interaction with a metal ion or effector ligand, BigR from X. fastidiosa was crystallized in native and selenomethionine (SeMet) labelled forms using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected from native and SeMet crystals to resolutions of 1.95 and 2.2 Å, respectively. Both crystals belong to space group P321 and contain one molecule per asymmetric unit.

  8. A versatile three/four crystal X-ray diffractometer for X-ray optical elements: Performance and applications

    DEFF Research Database (Denmark)

    Christensen, Finn Erland; Hornstrup, Allan; Jacobsen, E.

    1987-01-01

    A versatile X-ray diffractometer for the study of X-ray optical elements such as grazing incidence mirrors, crystals and X-ray gratings has been built and put into operation at the Danish Space Research Institute. The diffractrometer is built on a 1.5 m long granite bench with the X-ray source...... located at one end of the bench where it can be rotated around a fixed vertical axis. The beam defining elements are perfect crystals of Si, Ge or quartz. With these it is possible to define a highly collimated beam of a few arcsec fwhm in the scattering plane. Examples of measurements on various X...

  9. Performance of the x-ray free-electron laser oscillator with crystal cavity

    Science.gov (United States)

    Lindberg, R. R.; Kim, K.-J.; Shvyd'Ko, Yu.; Fawley, W. M.

    2011-01-01

    Simulations of the x-ray free-electron laser (FEL) oscillator are presented that include the frequency-dependent Bragg crystal reflectivity and the transverse diffraction and focusing using the two-dimensional FEL code GINGER. A review of the physics of Bragg crystal reflectors and the x-ray FEL oscillator is made, followed by a discussion of its numerical implementation in GINGER. The simulation results for a two-crystal cavity and realistic FEL parameters indicate ˜109 photons in a nearly Fourier-limited, ps pulse. Compressing the electron beam to 100 A and 100 fs results in comparable x-ray characteristics for relaxed beam emittance, energy spread, and/or undulator parameters, albeit in a larger radiation bandwidth. Finally, preliminary simulation results indicate that the four-crystal FEL cavity can be tuned in energy over a range of a few percent.

  10. Performance of the x-ray free-electron laser oscillator with crystal cavity

    Directory of Open Access Journals (Sweden)

    R. R. Lindberg

    2011-01-01

    Full Text Available Simulations of the x-ray free-electron laser (FEL oscillator are presented that include the frequency-dependent Bragg crystal reflectivity and the transverse diffraction and focusing using the two-dimensional FEL code GINGER. A review of the physics of Bragg crystal reflectors and the x-ray FEL oscillator is made, followed by a discussion of its numerical implementation in GINGER. The simulation results for a two-crystal cavity and realistic FEL parameters indicate ∼10^{9} photons in a nearly Fourier-limited, ps pulse. Compressing the electron beam to 100 A and 100 fs results in comparable x-ray characteristics for relaxed beam emittance, energy spread, and/or undulator parameters, albeit in a larger radiation bandwidth. Finally, preliminary simulation results indicate that the four-crystal FEL cavity can be tuned in energy over a range of a few percent.

  11. Picosecond X-ray diffraction from laser-irradiated crystals

    Energy Technology Data Exchange (ETDEWEB)

    Hironaka, Yoichiro; Yazaki, Akio; Kishimura, Hiroaki; Nakamura, Kazutaka G.; Kondo, Ken-ichi

    2002-09-30

    We performed time-resolved X-ray diffraction for laser-irradiated Si(1 1 1) single crystal. A tabletop TW laser system was used for the generation of the ultra-short pulsed X-rays. We discussed the generation of laser induced ultra-short pulsed X-rays concerning about broadening of diffracted signal due to the electron scattering in the pre-plasma. We measured laser induced acoustic wave propagation inside of Si crystal by the laser irradiation, and the maximum lattice strain of -1.05% was measured at the irradiation power density of 4.7x10{sup 9} W/cm{sup 2} with picosecond time resolution. Stress distribution analysis on the observed data under laser irradiation is also dised.

  12. Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni

    Energy Technology Data Exchange (ETDEWEB)

    Gonçalves, A. M. D.; Rêgo, A. T. [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal); Thomaz, M. [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal); Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2748-901 Oeiras (Portugal); Enguita, F. J., E-mail: fenguita@fm.ul.pt [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal); Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa (Portugal); Carrondo, M. A. [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal)

    2008-03-01

    Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. The first form belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with a tetramer in the asymmetric unit and unit-cell parameters a = 80.5, b = 119.0, c = 135.3 Å. The second form belongs to space group C2, with unit-cell parameters a = 121.4, b = 47.1, c = 97.8 Å, and contains a dimer in the asymmetric unit. Diffraction data have been collected from these crystal forms to 2.5 and 2.95 Å resolution, respectively.

  13. Improving Protein Crystal Quality by the Without-Oil Microbatch Method: Crystallization and Preliminary X-ray Diffraction Analysis of Glutathione Synthetase from Pseudoalteromonas haloplanktis

    Directory of Open Access Journals (Sweden)

    Antonella Albino

    2011-09-01

    Full Text Available Glutathione synthetases catalyze the ATP-dependent synthesis of glutathione from L-γ-glutamyl-L-cysteine and glycine. Although these enzymes have been sequenced and characterized from a variety of biological sources, their exact catalytic mechanism is not fully understood and nothing is known about their adaptation at extremophilic environments. Glutathione synthetase from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhGshB has been expressed, purified and successfully crystallized. An overall improvement of the crystal quality has been obtained by adapting the crystal growth conditions found with vapor diffusion experiments to the without-oil microbatch method. The best crystals of PhGshB diffract to 2.34 Å resolution and belong to space group P212121, with unit-cell parameters a = 83.28 Å, b = 119.88 Å, c = 159.82 Å. Refinement of the model, obtained using phases derived from the structure of the same enzyme from Escherichia coli by molecular replacement, is in progress. The structural determination will provide the first structural characterization of a psychrophilic glutathione synthetase reported to date.

  14. Design, syntheses, characterization and single crystal X-ray ...

    Indian Academy of Sciences (India)

    Administrator

    Design, syntheses, characterization and single crystal X-ray diffraction studies of multicomponent Zn-tetraphenylpor- phyrins: Novel building blocks for microporous crystalline solids. ATINDRA D SHUKLA 1, PARESH C DAVE 1, ERINGATHODI. SURESH 1, GOPAL PATHAK 2, AMITAVA DAS 1 and. PARTHASARATHI ...

  15. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    DOI 10.1007/s12039-015-0978-8. Synthesis, characterization, X-ray crystal structure, electrochemical evaluation and anti-cancer studies of a mixed ligand Cu(II) complex of (E)-N -((2-hydroxynaphthalen-1-yl)methylene)acetohydrazide. IRAN SHEIKHSHOAIEa, S YOUSEF EBRAHIMIPOURa,∗, MAHDIEH SHEIKHSHOAIEa,.

  16. Expression, purification, crystallization and preliminary X-ray crystallographic studies of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45.

    Science.gov (United States)

    Ravaud, Stéphanie; Watzlawick, Hildegard; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2005-01-01

    The trehalulose synthase (MutB) from Pseudomonas mesoacidophila MX-45, belonging to glycoside hydrolase family 13, catalyses the isomerization of sucrose to trehalulose (alpha-D-glucosylpyranosyl-1,1-D-fructofuranose) and isomaltulose (alpha-D-glucosylpyranosyl-1,6-D-fructofuranose) as main products and glucose and fructose in residual amounts from the hydrolytic reaction. To date, a three-dimensional structure of a sucrose isomerase that produces mainly trehalulose, as is the case for MutB, has been lacking. Crystallographic studies of this 64 kDa enzyme have therefore been initiated in order to contribute to the understanding of the molecular basis of sucrose decomposition, isomerization and of the selectivity of this enzyme that leads to the formation of different products. The MutB protein has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms have been obtained: one diffracts X-rays to 1.6 A resolution using synchrotron radiation and belongs to space group P1, with unit-cell parameters a = 63.8, b = 72.0, c = 82.2 A, alpha = 67.5, beta = 73.1, gamma = 70.8 degrees, while the other form diffracts to 1.8 A resolution using synchrotron radiation and belongs to space group P2(1), with unit-cell parameters a = 63.7, b = 85.9, c = 119.7 A, beta = 97.7 degrees. A molecular-replacement solution has been found using the structure of the isomaltulose synthase (PalI) from Klebsiella sp. LX3 as a search model.

  17. SYNCHROTRON X-RAY BASED CHARACTERIZATION OF CDZNTE CRYSTALS

    Energy Technology Data Exchange (ETDEWEB)

    Duff, M

    2006-09-28

    Synthetic CdZnTe or 'CZT' crystals can be used for the room temperature-based detection of {gamma}-radiation. Structural/morphological heterogeneities within CZT, such as twinning, inclusions, and polycrystallinity can affect detector performance. We used a synchrotron-based X-ray technique, specifically extended X-ray absorption fine-structure (EXAFS) spectroscopy, to determine whether there are differences on a local structural level between intact CZT of high and low radiation detector performance. These studies were complemented by data on radiation detector performance and transmission IR imaging. The EXAFS studies revealed no detectable local structural differences between the two types of CZT materials.

  18. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  19. Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Lapkouski, Mikalai [Institute of Physical Biology, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady (Czech Republic); Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady (Czech Republic); Panjikar, Santosh [EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg (Germany); Kuta Smatanova, Ivana; Csefalvay, Eva, E-mail: jindrova@greentech.cz [Institute of Physical Biology, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady (Czech Republic); Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady (Czech Republic)

    2007-07-01

    The purification, crystallization and preliminary diffraction analysis of the HsdR subunit of the EcoR124I endonuclease are described. EcoR124I is a multicomplex enzyme belonging to the type I restriction-modification system from Escherichia coli. Although EcoR124I has been extensively characterized biochemically, there is no direct structural information available about particular subunits. HsdR is a motor subunit that is responsible for ATP hydrolysis, DNA translocation and cleavage of the DNA substrate recognized by the complex. Recombinant HsdR subunit was crystallized using the sitting-drop vapour-diffusion method. Crystals belong to the primitive monoclinic space group, with unit-cell parameters a = 85.75, b = 124.71, c = 128.37 Å, β = 108.14°. Native data were collected to 2.6 Å resolution at the X12 beamline of EMBL Hamburg.

  20. Spatiotemporal response of crystals in x-ray Bragg diffraction

    Science.gov (United States)

    Shvyd'ko, Yuri; Lindberg, Ryan

    2012-10-01

    The spatiotemporal response of crystals in x-ray Bragg diffraction resulting from excitation by an ultrashort, laterally confined x-ray pulse is studied theoretically. The theory presents an extension of the analysis in symmetric reflection geometry [R. R. Lindberg and Y. V. Shvyd’ko, Phys. Rev. ST Accel. Beams 15, 050706 (2012)PRABFM1098-440210.1103/PhysRevSTAB.15.050706] to the generic case, which includes Bragg diffraction both in reflection (Bragg) and transmission (Laue) asymmetric scattering geometries. The spatiotemporal response is presented as a product of a crystal-intrinsic plane-wave spatiotemporal response function and an envelope function defined by the crystal-independent transverse profile of the incident beam and the scattering geometry. The diffracted wave fields exhibit amplitude modulation perpendicular to the propagation direction due to both angular dispersion and the dispersion due to Bragg’s law. The characteristic measure of the spatiotemporal response is expressed in terms of a few parameters: the extinction length, crystal thickness, Bragg angle, asymmetry angle, and the speed of light. Applications to self-seeding of hard x-ray free-electron lasers are discussed, with particular emphasis on the relative advantages of using either the Bragg or Laue scattering geometries. Intensity front inclination in asymmetric diffraction can be used to make snapshots of ultrafast processes with femtosecond resolution.

  1. Spatiotemporal response of crystals in x-ray Bragg diffraction

    Directory of Open Access Journals (Sweden)

    Yuri Shvyd’ko

    2012-10-01

    Full Text Available The spatiotemporal response of crystals in x-ray Bragg diffraction resulting from excitation by an ultrashort, laterally confined x-ray pulse is studied theoretically. The theory presents an extension of the analysis in symmetric reflection geometry [R. R. Lindberg and Y. V. Shvyd’ko, Phys. Rev. ST Accel. Beams 15, 050706 (2012PRABFM1098-440210.1103/PhysRevSTAB.15.050706] to the generic case, which includes Bragg diffraction both in reflection (Bragg and transmission (Laue asymmetric scattering geometries. The spatiotemporal response is presented as a product of a crystal-intrinsic plane-wave spatiotemporal response function and an envelope function defined by the crystal-independent transverse profile of the incident beam and the scattering geometry. The diffracted wave fields exhibit amplitude modulation perpendicular to the propagation direction due to both angular dispersion and the dispersion due to Bragg’s law. The characteristic measure of the spatiotemporal response is expressed in terms of a few parameters: the extinction length, crystal thickness, Bragg angle, asymmetry angle, and the speed of light. Applications to self-seeding of hard x-ray free-electron lasers are discussed, with particular emphasis on the relative advantages of using either the Bragg or Laue scattering geometries. Intensity front inclination in asymmetric diffraction can be used to make snapshots of ultrafast processes with femtosecond resolution.

  2. Crystal defect studies using x-ray diffuse scattering

    Energy Technology Data Exchange (ETDEWEB)

    Larson, B.C.

    1980-01-01

    Microscopic lattice defects such as point (single atom) defects, dislocation loops, and solute precipitates are characterized by local electronic density changes at the defect sites and by distortions of the lattice structure surrounding the defects. The effect of these interruptions of the crystal lattice on the scattering of x-rays is considered in this paper, and examples are presented of the use of the diffuse scattering to study the defects. X-ray studies of self-interstitials in electron irradiated aluminum and copper are discussed in terms of the identification of the interstitial configuration. Methods for detecting the onset of point defect aggregation into dislocation loops are considered and new techniques for the determination of separate size distributions for vacancy loops and interstitial loops are presented. Direct comparisons of dislocation loop measurements by x-rays with existing electron microscopy studies of dislocation loops indicate agreement for larger size loops, but x-ray measurements report higher concentrations in the smaller loop range. Methods for distinguishing between loops and three-dimensional precipitates are discussed and possibilities for detailed studies considered. A comparison of dislocation loop size distributions obtained from integral diffuse scattering measurements with those from TEM show a discrepancy in the smaller sizes similar to that described above.

  3. Crystallization and preliminary X-ray analysis of Der f 2, a potent allergen derived from the house dust mite (Dermatophagoides farinae)

    Science.gov (United States)

    Roeber, Dana; Achari, Aniruddha; Takai, Toshiro; Okumura, Yasushi; Scott, David L.

    2003-01-01

    Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophagoides sp.) are ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis and asthma associated with allergic reactions to these arthropods are frequently caused by relatively small (125-129 amino acids) mite proteins of unknown biological function. Der f 2, a major allergen from the mite D. farinae, has been recombinantly expressed, characterized and crystallized. The crystals belong to the tetragonal space group I4(1)22, with unit-cell parameters a = b = 95.2, c = 103.3 A. An essentially complete (97.2%) data set has been collected to 2.4 A at a synchrotron source. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pteronyssinus) failed, but preliminary searches using the crystalline Der p 2 atomic coordinates appear to be promising.

  4. Protein crystallization: Eluding the bottleneck of X-ray crystallography

    Science.gov (United States)

    Holcomb, Joshua; Spellmon, Nicholas; Zhang, Yingxue; Doughan, Maysaa; Li, Chunying; Yang, Zhe

    2017-01-01

    To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins. PMID:29051919

  5. X-ray Laue diffraction from crystals of xylose isomerase.

    OpenAIRE

    Farber, G. K.; Machin, P; Almo, S C; Petsko, G A; Hajdu, J.

    1988-01-01

    The Laue method (stationary crystal, polychromatic x-rays) was used to collect native and heavy-atom-derivative data on crystals of xylose isomerase (EC 5.3.1.5). These data were used to find the heavy-atom positions. The positions found by use of Laue data are the same as those found by use of monochromatic data collected on a diffractometer. These results confirm that Laue diffraction data sets, which can be obtained on a millisecond time scale, can be used to locate small molecules bound t...

  6. Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, M.; Nam, H; Carter, A; McCall, A; Rence, C; Bennett, A; Gurda, B; McKenna, R; Porter, M; et. al.

    2009-01-01

    Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetric unit capsid have been determined by molecular-replacement methods and structure determination is in progress.

  7. Crystallization and identification of the glycosylated moieties of two isoforms of the main allergen Hev b 2 and preliminary X-ray analysis of two polymorphs of isoform II

    Energy Technology Data Exchange (ETDEWEB)

    Fuentes-Silva, D. [Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Mendoza-Hernández, G. [Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Stojanoff, V. [Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY (United States); Palomares, L. A. [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Zenteno, E. [Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Torres-Larios, A. [Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Rodríguez-Romero, A., E-mail: adela@servidor.unam.mx [Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico)

    2007-09-01

    Crystallization of important glycoenzymes involved in IgE-mediated latex allergy. Latex from Hevea brasiliensis contains several allergenic proteins that are involved in type I allergy. One of them is Hev b 2, which is a β-1,3-glucanase enzyme that exists in different isoforms with variable glycosylation content. Two glucanase isoforms were isolated from trees of the GV-42 clone by gel filtration, affinity and ion-exchange chromatography. Isoform I had a carbohydrate content of about 20%, with N-linked N-acetyl-glucosamine, N-acetyl-galactosamine, fucose and galactose residues as the main sugars, while isoform II showed 6% carbohydrate content constisting of N-acetyl-glucosamine, fucose, mannose and xylose. Both isoforms were crystallized by the hanging-drop vapour-diffusion method. Isoform I crystals were grown using 0.2 M trisodium citrate dihydrate, 0.1 M Na HEPES pH 7.5 and 20%(v/v) 2-propanol, but these crystals were not appropriate for data collection. Isoform II crystals were obtained under two conditions and X-ray diffraction data were collected from both. In the first condition (0.2 M trisodium citrate, 0.1 M sodium cacodylate pH 6.5, 30% 2-propanol), crystals belonging to the tetragonal space group P4{sub 1} with unit-cell parameters a = b = 150.17, c = 77.41 Å were obtained. In the second condition [0.2 M ammonium acetate, 0.1 M trisodium citrate dihydrate pH 5.6, 30%(w/v) polyethylene glycol 4000] the isoform II crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 85.08, b = 89.67, c = 101.80 Å, β = 113.6°. Preliminary analysis suggests that there are four molecules of isoform II in both asymmetric units.

  8. 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

    The human type I allergic response is characterized by the presence of allergen-specific serum immunoglobulin E (IgE). Allergen-mediated cross-linking of receptor-bound IgE on the surface of mast cells and circulating basophils triggers the release of mediators, resulting in the development......, with unit-cell parameters a = 91.65, b = 99.14, c = 108.90 A, alpha = 105.7, beta = 98.32, gamma = 97.62 degrees, and diffract to 2.9 A resolution when analyzed at 100 K using synchrotron-generated X--rays....

  9. Graded SiGe crystals as X-ray collimators

    CERN Document Server

    Petrashen, P

    2001-01-01

    Many X-ray applications could benefit from a beam conditioner providing a parallel beam with a small cross-section. The limiting values may vary with an application, however, not a single commonly used X-ray optical device is able to achieve these two requirements simultaneously without a drastic loss of the primary beam intensity. The most promising way to overcome this limitation is using crystals with a gradient of the lattice parameter. Recent technological successes in growing high-perfection crystals of Ge-Si solid solutions [A. Erko, F. Schaefers, W. Gudat, N.V. Abrosimov, S.N. Rossolenko, V. Alex, W. Schroeder. Nucl. Instr. Meth. Phys. Res. A 374 (1996) 408] make this goal achievable. The high quality of these crystals is experimentally confirmed [S. Keitel, C. Malgrange, T. Niemueller, J.R. Schneider. Acta Crystallogr. A 55 (1999) 855]. This study shows that the gradient crystals allow making high-quality beam collimators overcoming the flux gain restrictions imposed by the flat or curved single crys...

  10. X-ray Crystal Spectrometers and Monochromators in Microanalysis.

    Science.gov (United States)

    Wittry, David B.; Barbi, Nicholas C.

    2001-03-01

    Castaing's successful implementation and application of the electron probe microanalyzer in 1950 stimulated a flurry of development activity around the world. The later versions of this instrument represented a truly international effort, with significant contributions by scientists from Europe, Asia, and North America. If the probe-forming system of the instrument was its heart, the X-ray wavelength spectrometer was its soul. This article reviews some of the history of spectrometer developments-through the "golden years" of microprobe development, namely the dozen or so years following the publication of Castaing's thesis, to the present. The basic physics of spectrometer and crystal design is reviewed. Early experimental devices, such as those developed by Castaing, Borovskii, Wittry, Duncumb, and Ogilvie are reported. Examples of commercial spectrometers such as those by ARL, MAC, Microspec, and Peak are described. Recent developments such as the combination of grazing-incidence optics with flat crystal spectrometers are noted, and the properties and uses of doubly curved crystals are discussed. Finally, the continued development of doubly curved crystal configurations, such as the "Wittry geometry" for scanning monochromators, and point-to-point focusing diffractors for producing small monochromatic X-ray probes to provide improved detection limits for microanalysis are considered.

  11. Purification, crystallization and preliminary X-ray analysis of the galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum JCM1217

    Energy Technology Data Exchange (ETDEWEB)

    Wada, Jun [Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan); Suzuki, Ryuichiro; Fushinobu, Shinya [Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Kitaoka, Motomitsu [National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 (Japan); Wakagi, Takayoshi; Shoun, Hirofumi [Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Ashida, Hisashi [Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan); Kumagai, Hidehiko; Katayama, Takane, E-mail: takane@ishikawa-pu.ac.jp [Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836 (Japan); Yamamoto, Kenji [Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan)

    2007-09-01

    Preliminary X-ray analysis of the galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from B. longum is described. A recombinant galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) from Bifidobacterium longum JCM1217 has been prepared and crystallized by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 0.01 M zinc sulfate, 0.1 M MES buffer pH 5.9–6.4 and 20–22%(v/v) PEG MME 550 in the presence of 5 mM disaccharide ligands. Suitable crystals grew after 10 d incubation at 293 K. The crystals belong to space group C222{sub 1}, with unit-cell parameters a = 106.3, b = 143.6, c = 114.6 Å for the lacto-N-biose I complex and a = 106.4, b = 143.4, c = 115.5 Å for the galacto-N-biose complex, and diffracted to 1.85 and 1.99 Å resolution, respectively.

  12. Crystallization and Identification of the Glycosylated Moieties of Two Isoforms of the Main Allergen Hev b 2 and Preliminary X-ray Analysis of Two Polymorphs of Isoform ll

    Energy Technology Data Exchange (ETDEWEB)

    Fuentes-Silva,D.; Mendoza-Hernandez, G.; Stojanoff, V.; Palomares, L.; Zenteno, E.; Torres-Larios, A.; Rodriguez-Romero, A.

    2007-01-01

    Latex from Hevea brasiliensis contains several allergenic proteins that are involved in type I allergy. One of them is Hev b 2, which is a {beta}-1,3-glucanase enzyme that exists in different isoforms with variable glycosylation content. Two glucanase isoforms were isolated from trees of the GV-42 clone by gel filtration, affinity and ion-exchange chromatography. Isoform I had a carbohydrate content of about 20%, with N-linked N-acetyl-glucosamine, N-acetyl-galactosamine, fucose and galactose residues as the main sugars, while isoform II showed 6% carbohydrate content consisting of N-acetyl-glucosamine, fucose, mannose and xylose. Both isoforms were crystallized by the hanging-drop vapor-diffusion method. Isoform I crystals were grown using 0.2 M trisodium citrate dihydrate, 0.1 M Na HEPES pH 7.5 and 20%(v/v) 2-propanol, but these crystals were not appropriate for data collection. Isoform II crystals were obtained under two conditions and X-ray diffraction data were collected from both. In the first condition (0.2 M trisodium citrate, 0.1 M sodium cacodylate pH 6.5, 30% 2-propanol), crystals belonging to the tetragonal space group P4{sub 1} with unit-cell parameters a = b = 150.17, c = 77.41 {angstrom} were obtained. In the second condition [0.2 M ammonium acetate, 0.1 M trisodium citrate dihydrate pH 5.6, 30%(w/v) polyethylene glycol 4000] the isoform II crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 85.08, b = 89.67, c = 101.80 {angstrom}, {beta}= 113.6{sup o}. Preliminary analysis suggests that there are four molecules of isoform II in both asymmetric units.

  13. Ultrafast X-ray diffraction of laser-irradiated crystals

    CERN Document Server

    Heimann, P A; Kang, I; Johnson, S; Missalla, T; Chang, Z; Falcone, R W; Schönlein, R W; Glover, T E; Padmore, H A

    2001-01-01

    Coherent acoustic phonons have been observed in the X-ray diffraction of a laser-excited InSb crystal. Modeling based on time-dependent dynamical diffraction theory has allowed the extraction of fundamental constants, such as the electron-acoustic phonon coupling time. A dedicated beamline for time-resolved studies has been developed at the Advanced Light Source with special considerations toward high transmission, low scattering and a wide photon energy range. The facility combines a bend magnet beamline, time-resolved detectors and a femtosecond laser system.

  14. A Preliminary Research on the Development of the Hard X-ray Imaging Telescope

    Science.gov (United States)

    Zheng, Chun-Xiao; Cai, Ming-Sheng; Hu, Yi-Ming; Huang, Yong-Yi; Gong, Yi-Zhong

    2014-10-01

    The hard X-ray imaging telescope based on the Fourier transform imaging technique is introduced. The double-layer parallel gratings are used to make the modulation and coding on the light emerging from a celestial X-ray source, the modulated light is acquired, to make the optoelectronic conversion by scintillation crystal detectors, and finally read out by the electronic system. The modulation collimator X-ray telescopes can be divided into two types: the spatial modulation and temporal modulation. The temporal modulation system requires the scanning motion of the detector system, but the spatial modulation system requires no motion. The technology of grating fabrication is investigated, and the basic structure design of the collimators is given. The principal compo- nents of the prototype hard X-ray imaging telescope of spatial modulation type are successfully developed, including the 8 CsI crystal detector modules (contain- ing photomultipliers or PMTs), 8-channel shaping amplifiers (two of them are prepared for experiments), and the data acquisition system. And the preliminary test results of the electronic system are also given.

  15. Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Cockayne syndrome protein A in complex with DNA damage-binding protein 1.

    Science.gov (United States)

    Meulenbroek, Elisabeth M; Pannu, Navraj S

    2012-01-01

    Cockayne syndrome protein A is one of the main components in mammalian transcription coupled repair. Here, the overproduction, purification and crystallization of human Cockayne syndrome protein A in complex with its interacting partner DNA damage binding protein 1 are reported. The complex was coproduced in insect cells, copurified and crystallized using sitting drops with PEG 3350 and sodium citrate as crystallizing agents. The crystals had unit-cell parameters a = b = 142.03, c = 250.19 Å and diffracted to 2.9 Å resolution on beamline ID14-1 at the European Synchrotron Radiation Facility. © 2012 International Union of Crystallography. All rights reserved.

  16. Expression, purification, crystallization and preliminary X-ray analysis of a C-terminal fragment of the Epstein–Barr virus ZEBRA protein

    Energy Technology Data Exchange (ETDEWEB)

    Morand, Patrice [European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble CEDEX 9 (France); Laboratoire de Virologie Moléculaire et Structurale, EA 2939, Université Joseph Fourier, Grenoble (France); Budayova-Spano, Monika [European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble CEDEX 9 (France); Perrissin, Monique [Laboratoire de Virologie Moléculaire et Structurale, EA 2939, Université Joseph Fourier, Grenoble (France); Müller, Christoph W., E-mail: mueller@embl-grenoble.fr; Petosa, Carlo [European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble CEDEX 9 (France)

    2006-03-01

    A C-terminal fragment of the Epstein–Barr virus lytic switch protein ZEBRA has been crystallized in complex with DNA. A C-terminal fragment of the Epstein–Barr virus immediate-early transcription factor ZEBRA has been expressed as a recombinant protein in Escherichia coli and purified to homogeneity. The fragment behaves as a dimer in solution, consistent with the presence of a basic region leucine-zipper (bZIP) domain. Crystals of the fragment in complex with a DNA duplex were grown by the hanging-drop vapour-diffusion technique using polyethylene glycol 4000 and magnesium acetate as crystallization agents. Crystals diffract to better than 2.5 Å resolution using synchrotron radiation (λ = 0.976 Å). Crystals belong to space group C2, with unit-cell parameters a = 94.2, b = 26.5, c = 98.1 Å, β = 103.9°.

  17. Crystallization and preliminary X-ray diffraction analysis of the tRNA-modification enzyme GidA from Aquifex aeolicus.

    Science.gov (United States)

    Osawa, Takuo; Inanaga, Hideko; Numata, Tomoyuki

    2009-05-01

    The 5-carboxymethylaminomethyl modification of uridine at the first position of the tRNA anticodon is crucial for accurate protein synthesis by stabilizing the correct codon-anticodon pairing on the ribosome. Two conserved enzymes, GidA and MnmE, are involved in this modification process. Aquifex aeolicus GidA was crystallized in two different crystal forms: forms I and II. These crystals diffracted to 3.2 and 2.3 A resolution, respectively, using synchrotron radiation at the Photon Factory. These crystals belonged to space groups I2(1)2(1)2(1) and P2(1) with unit-cell parameters a = 101.6, b = 213.3, c = 231.7 A and a = 119.4, b = 98.0, c = 129.6 A, beta = 90.002 degrees , respectively. The asymmetric units of these crystals are expected to contain two and four molecules, respectively.

  18. Crystallization and preliminary X-ray crystallographic analysis of the functional form of BinB binary toxin from Bacillus sphaericus.

    Science.gov (United States)

    Srisucharitpanit, Kanokporn; Yao, Min; Chimnaronk, Sarin; Promdonkoy, Boonhiang; Tanaka, Isao; Boonserm, Panadda

    2013-02-01

    The binary toxin from Bacillus sphaericus consists of two proteins, BinA and BinB, which work together to exert toxicity against mosquito larvae. BinB is proposed to be a receptor-binding domain and internalizes BinA into the midgut cells, resulting in toxicity via an unknown mechanism. The functional form of BinB has been successfully crystallized. The crystals of BinB diffracted to a resolution of 1.75 Å and belong to space group P6(2)22, with unit-cell parameters a = b = 95.2, c = 154.9 Å. Selenomethionine-substituted BinB (SeMetBinB) was prepared and crystallized for experimental phasing. The SeMetBinB crystal data were collected at a wavelength of 0.979 Å and diffracted to a resolution of 1.85 Å.

  19. Crystallization and preliminary X-ray diffraction analysis of eukaryotic α2-macroglobulin family members modified by methylamine, proteases and glycosidases

    DEFF Research Database (Denmark)

    Goulas, T; Garcia-Ferrer, I; García-Piqué, S

    2014-01-01

    α2-Macroglobulin (α2M) has many functions in vertebrate physiology. To understand the basis of such functions, high-resolution structural models of its conformations and complexes with interacting partners are required. In an attempt to grow crystals that diffract to high or medium resolution, we...... or with peptidases (thermolysin and chymotrypsin) rendered well-shaped crystals routinely diffracting below 7 Å in a reproducible manner....

  20. Crystallization and preliminary X-ray diffraction studies of the ferredoxin reductase component in the Rieske nonhaem iron oxygenase system carbazole 1,9a-dioxygenase

    Energy Technology Data Exchange (ETDEWEB)

    Ashikawa, Yuji; Uchimura, Hiromasa [Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Fujimoto, Zui [Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 (Japan); Inoue, Kengo [Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Noguchi, Haruko [Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Yamane, Hisakazu [Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Nojiri, Hideaki, E-mail: anojiri@mail.ecc.u-tokyo.ac.jp [Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2007-06-01

    The NAD(P)H:ferredoxin oxidoreductase in carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3 was crystallized and diffraction data were collected to 2.60 Å resolution. Carbazole 1,9a-dioxygenase (CARDO), which consists of an oxygenase component (CARDO-O) and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), catalyzes dihydroxylation at the C1 and C9a positions of carbazole. CARDO-R was crystallized at 277 K using the hanging-drop vapour-diffusion method with the precipitant PEG 8000. Two crystal types (types I and II) were obtained. The type I crystal diffracted to a maximum resolution of 2.80 Å and belonged to space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 158.7, c = 81.4 Å. The type II crystal was obtained in drops from which type I crystals had been removed; it diffracted to 2.60 Å resolution and belonged to the same space group, with unit-cell parameters a = b = 161.8, c = 79.5 Å.

  1. Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding region of the Streptococcus gordonii adhesin GspB

    Energy Technology Data Exchange (ETDEWEB)

    Pyburn, Tasia M.; Yankovskaya, Victoria; Bensing, Barbara A.; Cecchini, Gary; Sullam, Paul M.; Iverson, T.M. (VA); (Vanderbilt); (UCSF)

    2012-07-11

    The carbohydrate-binding region of the bacterial adhesin GspB from Streptococcus gordonii strain M99 (GspB{sub BR}) was expressed in Escherichia coli and purified using affinity and size-exclusion chromatography. Separate sparse-matrix screening of GspB{sub BR} buffered in either 20 mM Tris pH 7.4 or 20 mM HEPES pH 7.5 resulted in different crystallographic behavior such that different precipitants, salts and additives supported crystallization of GspB{sub BR} in each buffer. While both sets of conditions supported crystal growth in space group P2{sub 1}2{sub 1}2{sub 1}, the crystals had distinct unit-cell parameters of a = 33.3, b = 86.7, c = 117.9 {angstrom} for crystal form 1 and a = 34.6, b = 98.3, c = 99.0 {angstrom} for crystal form 2. Additive screening improved the crystals grown in both conditions such that diffraction extended to beyond 2 {angstrom} resolution. A complete data set has been collected to 1.3 {angstrom} resolution with an overall R{sub merge} value of 0.04 and an R{sub merge} value of 0.33 in the highest resolution shell.

  2. Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate

    Energy Technology Data Exchange (ETDEWEB)

    Mise, Takeshi; Matsunami, Hideyuki; Samatey, Fadel A.; Maruyama, Ichiro N., E-mail: ichi@oist.jp [Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495 (Japan)

    2014-08-27

    The periplasmic domain of the E. coli aspartate receptor Tar was cloned, expressed, purified and crystallized with and without bound ligand. The crystals obtained diffracted to resolutions of 1.58 and 1.95 Å, respectively. The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni{sup 2+}. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 were grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-Tar2 were grown and diffracted to resolutions of 1.95 and 1.58 Å, respectively. Crystals of apo-Tar1 and Asp-Tar1 adopted space group P4{sub 1}2{sub 1}2, while those of apo-Tar2 and Asp-Tar2 adopted space groups P2{sub 1}2{sub 1}2{sub 1} and C2, respectively.

  3. Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms

    Energy Technology Data Exchange (ETDEWEB)

    Park, Joon Kyu [Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650 (Korea, Republic of); School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Moon, Jin Ho [Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650 (Korea, Republic of); Kim, Jae-Hong [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Eunice EunKyeong, E-mail: eunice@kist.re.kr [Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650 (Korea, Republic of)

    2005-01-01

    Peptide deformylase (PDF) from B. cereus has been overexpressed, purified and crystallized in ligand-free and actinonin-bound forms. Diffraction data have been collected from these crystals to 1.7 and 2.0 Å resolution, respectively. In bacteria, protein expression initiates with an N-formyl group and this needs to be removed in order to ensure proper bacterial growth. These formylation and deformylation processes are unique to eubacteria; therefore, inhibition of these would provide a novel antibacterial therapy. Deformylation is carried out by peptide deformylase (PDF). PDF from Bacillus cereus, one of the major pathogenic bacteria, was cloned into expression plasmid pET-28a (Novagen), overexpressed in Escherichia coli BL21 (DE3) and purified to high quality. Crystals have been obtained of both ligand-free PDF and PDF to which actinonin, a highly potent naturally occurring inhibitor, is bound. Both crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 42.72, b = 44.04, c = 85.19 Å and a = 41.31, b = 44.56, c = 84.47 Å, respectively. Diffraction data were collected to 1.7 Å resolution for the inhibitor-free crystals and to 2.0 Å resolution for the actinonin-bound crystals.

  4. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of L-lactate dehydrogenase and its H171C mutant from Bacillus subtilis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yanfeng; Gao, Xiaoli (MSU)

    2012-08-31

    L-Lactate dehydrogenase (LDH) is an important enzyme involved in the last step of glycolysis that catalyzes the reversible conversion of pyruvate to L-lactate with the simultaneous oxidation of NADH to NAD{sup +}. In this study, wild-type LDH from Bacillus subtilis (BsLDH-WT) and the H171C mutant (BsLDH-H171C) were expressed in Escherichia coli and purified to near-homogeneity. BsLDH-WT was crystallized in the presence of fructose 1,6-bisphosphate (FBP) and NAD{sup +} and the crystal diffracted to 2.38 {angstrom} resolution. The crystal belonged to space group P3, with unit-cell parameters a = b = 171.04, c = 96.27 {angstrom}. BsLDH-H171C was also crystallized as the apoenzyme and in complex with NAD{sup +}, and data sets were collected to 2.20 and 2.49 {angstrom} resolution, respectively. Both BsLDH-H171C crystals belonged to space group P3, with unit-cell parameters a = b = 133.41, c = 99.34 {angstrom} and a = b = 133.43, c = 99.09 {angstrom}, respectively. Tetramers were observed in the asymmetric units of all three crystals.

  5. Expression, crystallization and preliminary X-ray analysis of the extracellular Ig modules I-IV and F3 modules I-III of the neural cell-adhesion molecule L1

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kasper, Christina; Kristensen, Ole

    2005-01-01

    Four amino-terminal immunoglobulin (Ig) modules and three fibronectin type III (F3) modules of the mouse neural cell-adhesion molecule L1 have been expressed in Drosophila S2 cells. The Ig modules I-IV of L1 crystallized in a trigonal space group, with unit-cell parameters a = b = 239.6, c = 99.3 A......, and the crystals diffracted X-rays to a resolution of about 3.5 A. The F3 modules I-III of L1 crystallized in a tetragonal space group, with unit-cell parameters a = b = 80.1, c = 131 A, and the crystals diffracted X-rays to 2.8 A resolution. This is a step towards the structure determination of the multimodular...

  6. Crystallization and preliminary X-ray crystallographic analysis of the heterodimeric crotoxin complex and the isolated subunits crotapotin and phospholipase A{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Santos, K. F.; Murakami, M. T. [Department of Physics, IBILCE/UNESP, Cristóvão Colombo 2265, CEP 15054-000, São José do Rio Preto, SP (Brazil); Cintra, A. C. O. [Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, SP (Brazil); Toyama, M. H.; Marangoni, S. [Departamento de Bioquímica, Universidade de Campinas, Campinas, SP (Brazil); Forrer, V. P.; Brandão Neto, J. R. [Laboratório Nacional de Luz Síncrotron, Campinas, SP (Brazil); Polikarpov, I. [Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP (Brazil); Arni, R. K., E-mail: arni@ibilce.unesp.br [Department of Physics, IBILCE/UNESP, Cristóvão Colombo 2265, CEP 15054-000, São José do Rio Preto, SP (Brazil); Center for Applied Toxinology, CEPID (Brazil)

    2007-04-01

    Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A{sub 2} and a catalytically inactive acidic phospholipase A{sub 2} analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained. Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A{sub 2} and a catalytically inactive acidic phospholipase A{sub 2} analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained. The crotoxin complex crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 38.2, b = 68.7, c = 84.2 Å, and diffracted to 1.75 Å resolution. The crystal of the phospholipase A{sub 2} domain belongs to the hexagonal space group P6{sub 1}22 (or its enantiomorph P6{sub 5}22), with unit-cell parameters a = b = 38.7, c = 286.7 Å, and diffracted to 2.6 Å resolution. The crotapotin crystal diffracted to 2.3 Å resolution; however, the highly diffuse diffraction pattern did not permit unambiguous assignment of the unit-cell parameters.

  7. Purification, Crystallization and Preliminary X-ray Characterization of Prunin-1, a Major Component of the Almond (Prunus dulcis) Allergen Amandin

    Energy Technology Data Exchange (ETDEWEB)

    Albillos, Silvia M.; Jin, Tengchuan; Howard, Andrew; Zhang, Yuzhu; Kothary, Mahendra H.; Fu, Tong-Jen (IIT); (US-FDA)

    2008-08-04

    The 11S globulins from plant seeds account for a number of major food allergens. Because of the interest in the structural basis underlying the allergenicity of food allergens, we sought to crystallize the main 11S seed storage protein from almond (Prunus dulcis). Prunin-1 (Pru1) was purified from defatted almond flour by water extraction, cryoprecipitation, followed by sequential anion exchange, hydrophobic interaction, and size exclusion chromatography. Single crystals of Pru1 were obtained in a screening with a crystal screen kit, using the hanging-drop vapor diffusion method. Diffraction quality crystals were grown after optimization. The Pru1 crystals diffracted to at least 3.0 {angstrom} and belong to the tetragonal space group P4{sub 1}22, with unit cell parameters of a = b = 150.912 {angstrom}, c = 165.248 {angstrom}. Self-rotation functions and molecular replacement calculations showed that there are three molecules in the asymmetry unit with water content of 51.41%. The three Pru1 protomers are related by a noncrystallographic 3-fold axis and they form a doughnut-shaped trimer. Two prunin trimers form a homohexamer. Elucidation of prunin structure will allow further characterization of the allergenic features of the 11S protein allergens at the molecular level.

  8. Purification, crystallization and preliminary X-ray characterization of prunin-1, a major component of the almond (Prunus dulcis) allergen amandin.

    Science.gov (United States)

    Albillos, Silvia M; Jin, Tengchuan; Howard, Andrew; Zhang, Yuzhu; Kothary, Mahendra H; Fu, Tong-Jen

    2008-07-09

    The 11S globulins from plant seeds account for a number of major food allergens. Because of the interest in the structural basis underlying the allergenicity of food allergens, we sought to crystallize the main 11S seed storage protein from almond ( Prunus dulcis). Prunin-1 (Pru1) was purified from defatted almond flour by water extraction, cryoprecipitation, followed by sequential anion exchange, hydrophobic interaction, and size exclusion chromatography. Single crystals of Pru1 were obtained in a screening with a crystal screen kit, using the hanging-drop vapor diffusion method. Diffraction quality crystals were grown after optimization. The Pru1 crystals diffracted to at least 3.0 A and belong to the tetragonal space group P4(1)22, with unit cell parameters of a = b = 150.912 A, c = 165.248 A. Self-rotation functions and molecular replacement calculations showed that there are three molecules in the asymmetry unit with water content of 51.41%. The three Pru1 protomers are related by a noncrystallographic 3-fold axis and they form a doughnut-shaped trimer. Two prunin trimers form a homohexamer. Elucidation of prunin structure will allow further characterization of the allergenic features of the 11S protein allergens at the molecular level.

  9. Crystallization and preliminary X-ray crystallographic analysis of a conserved domain in plants and prokaryotes from Pyrococcus horikoshii OT3

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Linyen; Nakano, Hiroaki; Uchiyama, Susumu; Fujimoto, Satoru; Matsunaga, Sachihiro [Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871 Osaka (Japan); Nakamura, Shota; Kobayashi, Yuji; Ohkubo, Tadayasu [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, 565-0871 Osaka (Japan); Fukui, Kiichi, E-mail: kfukui@bio.eng.osaka-u.ac.jp [Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871 Osaka (Japan)

    2005-04-01

    A plant- and prokaryote-conserved domain (PPC) has been crystallized. The crystal diffracted to 1.7 Å resolution and belonged to space group P6{sub 3}22. A plant- and prokaryote-conserved domain (PPC) has previously been found in AT-hook motif nuclear localized protein 1 (AHL1) localized in the nuclear matrix of Arabidopsis thaliana (AtAHL1). AtAHL1 has a DNA-binding function. Mutation analyses of AtAHL1 has previously revealed that the hydrophobic region of the PPC domain is essential for its nuclear localization. In this study, the PPC of the hyperthermophilic archaebacterium Pyrococcus horikoshii (PhPPC) was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 53.69, c = 159.2 Å. Data were obtained at 100 K, with diffraction being observed to a resolution of 1.7 Å. A complete data set from crystals of the SeMet-substituted protein was also obtained.

  10. Overproduction, purification, crystallization and preliminary X-ray analysis of the peroxiredoxin domain of a larger natural hybrid protein from Thermotoga maritima

    Energy Technology Data Exchange (ETDEWEB)

    Barbey, Carole, E-mail: carole.barbey@smbh.univ-paris13.fr [Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny CEDEX (France); Rouhier, Nicolas [Unité Mixte de Recherches 1136 INRA UHP (Interaction Arbres Microorganismes), IFR 110, Nancy Université BP 239, 54506 Vandoeuvre-lès-Nancy CEDEX (France); Haouz, Ahmed [Plate-forme de Cristallogenèse et Diffraction des Rayons X, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris (France); Navaza, Alda [Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny CEDEX (France); Jacquot, Jean-Pierre [Unité Mixte de Recherches 1136 INRA UHP (Interaction Arbres Microorganismes), IFR 110, Nancy Université BP 239, 54506 Vandoeuvre-lès-Nancy CEDEX (France); Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny CEDEX (France)

    2008-01-01

    Crystals of the peroxiredoxin domain of a larger natural hybrid protein from T. maritima were obtained which diffracted to 2.9 Å resolution on a synchrotron source. Thermotoga maritima contains a natural hybrid protein constituted of two moieties: a peroxiredoxin domain at the N-terminus and a nitroreductase domain at the C-terminus. The peroxiredoxin (Prx) domain has been overproduced and purified from Escherichia coli cells. The recombinant Prx domain, which is homologous to bacterial Prx BCP and plant Prx Q, folds properly into a stable protein that possesses biological activity. The recombinant protein was crystallized and synchrotron data were collected to 2.9 Å resolution. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 176.67, c = 141.20 Å.

  11. Expression, purification, crystallization and preliminary X-ray characterization of a putative glycosyltransferase of the GT-A fold found in mycobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Fulton, Zara; Crellin, Paul K.; Brammananth, Rajini; Zaker-Tabrizi, Leyla; Coppel, Ross L.; Rossjohna, Jamie; Beddoe, Travis (Monash)

    2008-05-28

    Glycosidic bond formation is a ubiquitous enzyme-catalysed reaction. This glycosyltransferase-mediated process is responsible for the biosynthesis of innumerable oligosaccharides and glycoconjugates and is often organism- or cell-specific. However, despite the abundance of genomic information on glycosyltransferases (GTs), there is a lack of structural data for this versatile class of enzymes. Here, the cloning, expression, purification and crystallization of an essential 329-amino-acid (34.8 kDa) putative GT of the classic GT-A fold implicated in mycobacterial cell-wall biosynthesis are reported. Crystals of MAP2569c from Mycobacterium avium subsp. paratuberculosis were grown in 1.6 M monoammonium dihydrogen phosphate and 0.1 M sodium citrate pH 5.5. A complete data set was collected to 1.8 {angstrom} resolution using synchrotron radiation from a crystal belonging to space group P4{sub 1}2{sub 1}2.

  12. Crystallization and preliminary X-ray analysis of a novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix.

    Science.gov (United States)

    Satomura, Takenori; Sakuraba, Haruhiko; Hara, Yusuke; Ohshima, Toshihisa

    2010-11-01

    A novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the tetragonal space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2, with unit-cell parameters a = b = 61.1, c = 276.3 Å, and diffracted to 2.87 Å resolution using a Cu Kα rotating-anode generator with an R-AXIS VII detector. The asymmetric unit contained one protein molecule, giving a crystal volume per enzyme mass (V(M)) of 2.75 Å(3) Da(-1) and a solvent content of 55.3%.

  13. Purification, crystallization and preliminary X-ray diffraction analysis of a soluble variant of the monoglyceride lipase Yju3p from the yeast Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Rengachari, Srinivasan; Aschauer, Philipp; Sturm, Christian; Oberer, Monika, E-mail: m.oberer@uni-graz.at [University of Graz, Humboldtstrasse 50/3, 8010 Graz (Austria)

    2015-01-28

    A soluble variant of the monoglyceride lipase Yju3p was successfully expressed, purified and crystallized. Diffraction data were collected to 2.4 Å resolution. The protein Yju3p is the orthologue of monoglyceride lipases in the yeast Saccharomyces cerevisiae. A soluble variant of this lipase termed s-Yju3p (38.3 kDa) was generated and purified to homogeneity by affinity and size-exclusion chromatography. s-Yju3p was crystallized in a vapour-diffusion setup at 293 K and a complete data set was collected to 2.4 Å resolution. The crystal form was orthorhombic (space group P2{sub 1}2{sub 1}2{sub 1}), with unit-cell parameters a = 77.2, b = 108.6, c = 167.7 Å. The asymmetric unit contained four molecules with a solvent content of 46.4%.

  14. Crystallization and X-ray diffraction analysis of a catalytic domain of hyperthermophilic chitinase from Pyrococcus furiosus

    Energy Technology Data Exchange (ETDEWEB)

    Mine, Shouhei; Nakamura, Tsutomu [National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan); Hirata, Kunio [RIKEN/SPring-8, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Ishikawa, Kazuhiko; Hagihara, Yoshihisa; Uegaki, Koichi, E-mail: k-uegaki@aist.go.jp [National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan)

    2006-08-01

    The expression, purification and preliminary X-ray diffraction analysis of a catalytic domain of a chitinase from P. furiosus is reported. The crystallization and preliminary X-ray diffraction analysis of a catalytic domain of chitinase (PF1233 gene) from the hyperthermophilic archaeon Pyrococcus furiosus is reported. The recombinant protein, prepared using an Escherichia coli expression system, was crystallized by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected at the undulator beamline BL44XU at SPring-8 to a resolution of 1.50 Å. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 90.0, b = 92.8, c = 107.2 Å.

  15. Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix.

    Science.gov (United States)

    Shibahara, Takenori; Satomura, Takenori; Kawakami, Ryushi; Ohshima, Toshihisa; Sakuraba, Haruhiko

    2011-11-01

    A dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 63.4, b = 119.4, c = 70.2 Å, β = 112.0°, and diffracted to 2.0 Å resolution on the BL26B1 beamline at SPring-8. The overall R(merge) was 4.5% and the completeness was 99.8%. © 2011 International Union of Crystallography. All rights reserved.

  16. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of macrophage growth locus A (MglA) protein from Francisella tularensis

    Energy Technology Data Exchange (ETDEWEB)

    Subburaman, P.; Austin, B.P.; Shaw, G.X.; Waugh, D.S.; Ji, X. (NCI)

    2010-11-03

    Francisella tularensis, a potential bioweapon, causes a rare infectious disease called tularemia in humans and animals. The macrophage growth locus A (MglA) protein from F. tularensis associates with RNA polymerase to positively regulate the expression of multiple virulence factors that are required for its survival and replication within macrophages. The MglA protein was overproduced in Escherichia coli, purified and crystallized. The crystals diffracted to 7.5 {angstrom} resolution at the Advanced Photon Source, Argonne National Laboratory and belonged to the hexagonal space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 125, c = 54 {angstrom}.

  17. Crystallization and preliminary X-ray diffraction analysis of the small subunit of the heterodimeric restriction endonuclease R.BspD6I

    Energy Technology Data Exchange (ETDEWEB)

    Kachalova, Galina S. [Max-Planck Unit for Structural Molecular Biology, Hamburg 22607 (Germany); Yunusova, Alfiya K.; Artyukh, Rimma I.; Rogulin, Eugeny A.; Perevyazova, Tatyana A.; Zheleznaya, Ludmila A. [Institute of Theoretical and Experimental Biophysics, Pushchino 142290 (Russian Federation); Matvienko, Nickolay I. [Institute of Protein Research, Pushchino 14229 (Russian Federation); Bartunik, Hans D., E-mail: bartunik@mpghdb.desy.de [Max-Planck Unit for Structural Molecular Biology, Hamburg 22607 (Germany)

    2007-09-01

    The crystallization of the small subunit of the heterodimeric restriction endonuclease R.BspD6I and diffraction data collection to 1.5 Å resolution are reported. The heterodimeric restriction endonuclease R.BspD6I is composed of a small subunit with a cleavage site and a large subunit, containing a recognition domain and a cleavage domain, that may function separately as a monomeric nicking endonuclease. Here, the crystallization of the small subunit and diffraction data collection to 1.5 Å resolution are reported.

  18. Expression, crystallization and preliminary X-ray analysis of the extracellular Ig modules I–IV and F3 modules I–III of the neural cell-adhesion molecule L1

    Energy Technology Data Exchange (ETDEWEB)

    Kulahin, Nikolaj, E-mail: kulahin@plab.ku.dk [Protein Laboratory, Institute of Molecular Pathology, Panum Institute, Blegdamsvej 3C, DK-2200 Copenhagen (Denmark); Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen (Denmark); Kasper, Christina; Kristensen, Ole; Kastrup, Jette Sandholm [Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen (Denmark); Berezin, Vladimir; Bock, Elisabeth [Protein Laboratory, Institute of Molecular Pathology, Panum Institute, Blegdamsvej 3C, DK-2200 Copenhagen (Denmark); Gajhede, Michael [Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen (Denmark); Protein Laboratory, Institute of Molecular Pathology, Panum Institute, Blegdamsvej 3C, DK-2200 Copenhagen (Denmark)

    2005-09-01

    Mouse L1 modules Ig I–IV and F3 I–III were crystallized. The crystals diffracted X-rays to 3.5 and 2.8 Å resolution, respectively. Four amino-terminal immunoglobulin (Ig) modules and three fibronectin type III (F3) modules of the mouse neural cell-adhesion molecule L1 have been expressed in Drosophila S2 cells. The Ig modules I–IV of L1 crystallized in a trigonal space group, with unit-cell parameters a = b = 239.6, c = 99.3 Å, and the crystals diffracted X-rays to a resolution of about 3.5 Å. The F3 modules I–III of L1 crystallized in a tetragonal space group, with unit-cell parameters a = b = 80.1, c = 131 Å, and the crystals diffracted X-rays to 2.8 Å resolution. This is a step towards the structure determination of the multimodular constructs of the neural cell-adhesion molecule L1 in order to understand the function of L1 on a structural basis.

  19. X-ray wavefront modeling of Bragg diffraction from crystals

    Science.gov (United States)

    Sutter, John P.

    2011-09-01

    The diffraction of an X-ray wavefront from a slightly distorted crystal can be modeled by the Takagi-Taupin theory, an extension of the well-known dynamical diffraction theory for perfect crystals. Maxwell's equations applied to a perturbed periodic medium yield two coupled differential equations in the incident and diffracted amplitude. These equations are discretized for numerical calculation into the determination of the two amplitudes on the points of an integration mesh, beginning with the incident amplitudes at the crystal's top surface. The result is a set of diffracted amplitudes on the top surface (in the Bragg geometry) or the bottom surface (in the Laue geometry), forming a wavefront that in turn can be propagated through free space using the Fresnel- Huygens equations. The performance of the Diamond Light Source I20 dispersive spectrometer has here been simulated using this method. Methods are shown for transforming displacements calculated by finite element analysis into local lattice distortions, and for efficiently performing 3-D linear interpolations from these onto the Takagi-Taupin integration mesh, allowing this method to be extended to crystals under thermal load or novel mechanical bender designs.

  20. Crystallization and preliminary X-ray crystallographic analysis of MbtI, a protein essential for siderophore biosynthesis in Mycobacterium tuberculosis.

    Science.gov (United States)

    Harrison, Anthony J; Ramsay, Rochelle J; Baker, Edward N; Lott, J Shaun

    2005-01-01

    Mycobacterium tuberculosis, the causative agent of tuberculosis, depends on the secretion of salicylate-based siderophores called mycobactins for the acquisition of extracellular iron, which is essential for the growth and virulence of the bacterium. The protein MbtI is thought to be the isochorismate synthase enzyme responsible for the conversion of chorismate to isochorismate, the first step in the salicylate production required for mycobactin biosynthesis. MbtI has been overexpressed in Escherichia coli, purified and crystallized. The crystals diffract to a maximum resolution of 1.8 A. They belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.8, b = 163.4, c = 194.9 A, consistent with the presence of either two, three or four molecules in the asymmetric unit.

  1. Cloning, expression, crystallization and preliminary X-ray studies of the ferredoxin-NAD(P)+ reductase from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.

    Science.gov (United States)

    Liauw, Pasqual; Mashiba, Tomohiro; Kopczak, Marta; Wiegand, Katrin; Muraki, Norifumi; Kubota, Hisako; Kawano, Yusuke; Ikeuchi, Masahiko; Hase, Toshiharu; Rögner, Matthias; Kurisu, Genji

    2012-09-01

    Ferredoxin-NADP(+) reductase (FNR) is a flavoenzyme that catalyses the reduction of NADP(+) in the final step of the photosynthetic electron-transport chain. FNR from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TeFNR) contains an additional 9 kDa domain at its N-terminus relative to chloroplastic FNRs and is more thermostable than those from mesophilic cyanobacteria. With the aim of understanding the structural basis of the thermostability of TeFNR and assigning a structural role to the small additional domain, the gene encoding TeFNR with and without an additional domain was engineered for heterologous expression and the recombinant proteins were purified and crystallized. Crystals of TeFNR without the additional domain belonged to space group P2(1), with unit-cell parameters a = 55.05, b = 71.66, c = 89.73 Å, α = 90, β = 98.21, γ = 90°.

  2. Crystallization and preliminary X-ray analysis of the complex of the first von Willebrand type C domain bound to bone morphogenetic protein 2

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Li-yan; Zhang, Jin-li [Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany); Kotzsch, Alexander [Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut der Universität Würzburg, Julius-von-Sachs Platz 2, D-97082 Würzburg (Germany); Sebald, Walter [Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany); Rudolf-Virchow-Zentrum (DFG Forschungszentrum) der Universität Würzburg, Versbacher Strasse 9, D-97070 Würzburg (Germany); Mueller, Thomas D., E-mail: mueller@botanik.uni-wuerzburg.de [Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut der Universität Würzburg, Julius-von-Sachs Platz 2, D-97082 Würzburg (Germany); Rudolf-Virchow-Zentrum (DFG Forschungszentrum) der Universität Würzburg, Versbacher Strasse 9, D-97070 Würzburg (Germany); Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany)

    2008-04-01

    Crystals of the complex of the first von Willebrand type C domain (VWC1) of crossveinless 2 (CV2) bound to bone morphogenetic protein 2 (BMP2) exist in two tetragonal crystal forms belonging to either space group P4{sub 1}2{sub 1}2 or I4{sub 1}, with one complete BMP2 dimer and two CV2 VWC1 domains per asymmetric unit, and diffract to 2.6 Å resolution. Crossveinless 2 (CV2) is a member of the chordin family, a protein superfamily that modulates the activity of bone morphogenetic proteins such as BMP2. The BMPs represent a large group of secreted proteins that control many steps during embryonal development and in tissue and organ homeostasis in the adult organism. The gene encoding the first von Willebrand type C domain (VWC1) of CV2 was cloned, expressed in Escherichia coli and purified to homogeneity. The binary complex of CV2 VWC1 and BMP2 was purified and subjected to crystallization. Crystals of SeMet-labelled proteins were obtained in two different forms belonging to the tetragonal space groups P4{sub 1}2{sub 1}2 and I4{sub 1}, with unit-cell parameters a = b = 86.7, c = 139.2 Å and a = b = 83.7, c = 139.6 Å, respectively. Initial analysis suggests that a complete binary complex consisting of one BMP2 dimer bound to two CV2 VWC1 domains is present in the asymmetric unit.

  3. Crystallization and preliminary X-ray analysis of (R)-specific enoyl-CoA hydratase from Aeromonas caviae involved in polyhydroxyalkanoate biosynthesis.

    Science.gov (United States)

    Hisano, T; Fukui, T; Iwata, T; Doi, Y

    2001-01-01

    Dimeric (R)-specific enoyl-coenzyme A (CoA) hydratase from Aeromonas caviae catalyzes the hydration of trans-2-enoyl-CoAs with carbon lengths of 4-6 to yield their corresponding (R)-3-hydroxyacyl-CoAs and is essential for polyhydroxyalkanoate (PHA) biosynthesis. The enzyme has been crystallized by vapour diffusion against a reservoir solution containing 20% polyethylene glycol 4000, 5% 2-propanol and 20 mM HEPES pH 7.0 at 298 K. Crystals belong to the monoclinic space group C2, with unit-cell parameters a = 111.54 (3), b = 59.29 (1), c = 47.27 (4) A, beta = 113.04 (2) degrees and contain a dimeric molecule in the asymmetric unit. Flash-cooling of a crystal at 100 K alters its unit-cell parameters to a = 109.82 (7), b = 57.98 (6), c = 46.84 (2) A, beta = 112.71 (3) degrees. Native data to a resolution of 1.7 A have been collected with 94.5% completeness and an R(merge) of 4.0% under cryogenic (100 K) conditions using synchrotron radiation.

  4. Crystallization and preliminary X-ray crystallographic analysis of MbtI, a protein essential for siderophore biosynthesis in Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, Anthony J. [School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Ramsay, Rochelle J. [Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Baker, Edward N.; Lott, J. Shaun, E-mail: s.lott@auckland.ac.nz [School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland (New Zealand)

    2005-01-01

    MbtI, the putative isochorismate synthase essential for siderophore biosynthesis in M. tuberculosis, has been crystallized. Diffraction data have been collected to 1.8 Å resolution. Mycobacterium tuberculosis, the causative agent of tuberculosis, depends on the secretion of salicylate-based siderophores called mycobactins for the acquisition of extracellular iron, which is essential for the growth and virulence of the bacterium. The protein MbtI is thought to be the isochorismate synthase enzyme responsible for the conversion of chorismate to isochorismate, the first step in the salicylate production required for mycobactin biosynthesis. MbtI has been overexpressed in Escherichia coli, purified and crystallized. The crystals diffract to a maximum resolution of 1.8 Å. They belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 51.8, b = 163.4, c = 194.9 Å, consistent with the presence of either two, three or four molecules in the asymmetric unit.

  5. Crystallization and preliminary X-ray crystallographic studies of CrArsM, an arsenic(III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii.

    Science.gov (United States)

    Packianathan, Charles; Pillai, Jitesh K; Riaz, Ahmed; Kandavelu, Palani; Sankaran, Banumathi; Rosen, Barry P

    2014-10-01

    Arsenic is one the most toxic environmental substances. Arsenic is ubiquitous in water, soil and food, and ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. Arsenic(III) S-adenosylmethionine methyltransferases (AS3MT in animals and ArsM in microbes) are key enzymes of arsenic biotransformation, catalyzing the methylation of inorganic arsenite to give methyl, dimethyl and trimethyl products. Arsenic methyltransferases are found in members of every kingdom from bacteria to humans (EC 2.1.1.137). In the human liver, hAS3MT converts inorganic arsenic into more toxic and carcinogenic forms. CrArsM, an ortholog of hAS3MT from the eukaryotic green alga Chlamydomonas reinhardtii, was purified by chemically synthesizing the gene and expressing it in Escherichia coli. Synthetic purified CrArsM was crystallized in an unliganded form. Crystals were obtained by the hanging-drop vapor-diffusion method. The crystals belonged to space group R3:H, with unit-cell parameters a = b = 157.8, c = 95.4 Å, γ = 120° and two molecules in the asymmetric unit. Complete data sets were collected and processed to a resolution of 2.40 Å.

  6. Purification, crystallization and preliminary X-ray crystallographic analysis of the archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3

    Energy Technology Data Exchange (ETDEWEB)

    Lokanath, Neratur K.; Kunishima, Naoki, E-mail: kunisima@spring8.or.jp [Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan)

    2006-08-01

    The archaeal phosphoglycerate mutase PH0037 from P. horikoshii OT3 has been crystallized in space group R32, with unit-cell parameters a = 155.62, c = 230.35 Å. A 2.2 Å resolution data was collected at SPring-8 beamline BL26B1. Phosphoglycerate mutases catalyze the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and gluconeogenesis pathways. The archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3 has been overexpressed in Escherichia coli and purified. Crystals were obtained using the oil-microbatch method at 291 K. A native data set extending to a resolution of 2.2 Å has been collected and processed in space group R32. Assuming the presence of a dimer in the asymmetric unit, the V{sub M} value is calculated to be 3.0 Å{sup 3} Da{sup −1}, consistent with the dynamic light-scattering experiment result, which shows a dimeric state of the protein in solution. Molecular-replacement trials using the crystal structure of Bacilllus stearothermophilus phosphoglycerate mutase as a search model did not provide a satisfactory solution, indicating substantially different structures of these two phophoglycerate mutases.

  7. Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction.

    Science.gov (United States)

    Hughes, Ronny C; Coates, Leighton; Blakeley, Matthew P; Tomanicek, Steve J; Langan, Paul; Kovalevsky, Andrey Y; García-Ruiz, Juan M; Ng, Joseph D

    2012-12-01

    Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a=106.11, b=95.46, c=113.68 Å, α=γ=90.0, β=98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure-function and mechanism studies of IPPase.

  8. Predicted and preliminary evaluation of the X-ray performance of the AXAF Technology Mirror Assembly

    Science.gov (United States)

    Van Speybroeck, Leon; Schwartz, Daniel; Reid, Paul; Bilbro, James

    1989-01-01

    The fabrication of the Technology Mirror Assembly (TMA) is complete, and performance predictions were made based upon mechanical and visible light measurements of the surface properties. An X-ray calibration program has been executed, and a preliminary analysis of a portion of the data is presented. The X-ray image distribution results are in reasonable agreement with the performance predictions which were calculated prior the start of the X-ray tests. The measured X-ray imaging performance approaches that expected for the Advanced X-ray Astrophysics Facility (AXAF).

  9. Crystallization via tubing microfluidics permits both in situ and ex situ X-ray diffraction.

    Science.gov (United States)

    Gerard, Charline J J; Ferry, Gilles; Vuillard, Laurent M; Boutin, Jean A; Chavas, Leonard M G; Huet, Tiphaine; Ferte, Nathalie; Grossier, Romain; Candoni, Nadine; Veesler, Stéphane

    2017-10-01

    A microfluidic platform was used to address the problems of obtaining diffraction-quality crystals and crystal handling during transfer to the X-ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X-ray data were collected both in situ and ex situ.

  10. Crystallization and preliminary X-ray crystallographic analysis of the small subunit of the heterodimeric laccase POXA3b from Pleurotus ostreatus.

    Science.gov (United States)

    Ferraroni, Marta; Scozzafava, Andrea; Ullah, Sana; Tron, Thierry; Piscitelli, Alessandra; Sannia, Giovanni

    2014-01-01

    Laccases are multicopper oxidases of great biotechnological potential. While laccases are generally monomeric glycoproteins, the white-rot fungus Pleurotus ostreatus produces two closely related heterodimeric isoenzymes composed of a large subunit, homologous to the other fungal laccases, and a small subunit. The sequence of the small subunit does not show significant homology to any other protein or domain of known function and consequently its function is unknown. The highest similarity to proteins of known structure is to a putative enoyl-CoA hydratase/isomerase from Acinetobacter baumannii, which shows an identity of 27.8%. Diffraction-quality crystals of the small subunit of the heterodimeric laccase POXA3b (sPOXA3b) from P. ostreatus were obtained using the sitting-drop vapour-diffusion method at 294 K from a solution consisting of 1.8 M sodium formate, 0.1 M Tris-HCl pH 8.5. The crystals belonged to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = 126.6, c = 53.9 Å. The asymmetric unit contains two molecules related by a noncrystallographic twofold axis. A complete data set extending to a maximum resolution of 2.5 Å was collected at 100 K using a wavelength of 1.140 Å.

  11. Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp. PCC 7120.

    Science.gov (United States)

    Narikawa, Rei; Muraki, Norifumi; Shiba, Tomoo; Ikeuchi, Masahiko; Kurisu, Genji

    2009-02-01

    Cyanobacteriochromes form a recently defined superfamily of tetrapyrrole-based photoreceptors that are distantly related to conventional red/far-red photoreceptor phytochromes. Among these molecules, AnPixJ from Anabaena sp. PCC 7120 is a novel photoreceptor that shows reversible photoconversion between green-absorbing and red-absorbing forms, which is in contrast to the properties of conventional phytochromes. In order to better understand the structural basis of this unique photoconversion mechanism, the chromophore-binding domain of AnPixJ (AnPixJ-GAF2) was heterologously overproduced and purified, and crystallization of both forms was attempted. Blue crystals of the red-absorbing form of AnPixJ-GAF2 were successfully obtained; they belonged to space group P4(3)2(1)2 and contained one monomer per asymmetric unit. Diffraction data were collected to a resolution of 1.8 A using synchrotron-radiation beamline BL-5A at the Photon Factory.

  12. Some Aspects of Crystal Centering During X-ray High-throughput Protein Crystallography Experiment

    Science.gov (United States)

    Gaponov, Yu. A.; Matsugaki, N.; Sasajima, K.; Igarashi, N.; Wakatsuki, S.

    A set of algorithms and procedures of a crystal loop centering during X-ray high-throughput protein crystallography experiment has been designed and developed. A simple algorithm of the crystal loop detection and preliminary recognition has been designed and developed. The crystal loop detection algorithm is based on finding out the crystal loop ending point (opposite to the crystal loop pin) using image cross section (digital image column) profile analysis. The crystal loop preliminary recognition procedure is based on finding out the crystal loop sizes and position using image cross section profile analysis. The crystal loop fine recognition procedure based on Hooke-Jeeves pattern search method with an ellipse as a fitting pattern has been designed and developed. The procedure of restoring missing coordinate of the crystal loop is described. Based on developed algorithms and procedures the optimal auto-centering procedure has been designed and developed. A procedure of optimal manual crystal centering (Two Clicks Procedure) has been designed and developed. Developed procedures have been integrated into control software system PCCS installed at crystallography beamlines Photon Factory BL5A and PF-AR NW12, KEK.

  13. Structural Characterization of Doped GaSb Single Crystals by X-ray Topography

    Energy Technology Data Exchange (ETDEWEB)

    Honnicke, M.G.; Mazzaro, I.; Manica, J.; Benine, E.; M da Costa, E.; Dedavid, B. A.; Cusatis, C.; Huang, X. R.

    2009-09-13

    We characterized GaSb single crystals containing different dopants (Al, Cd and Te), grown by the Czochralski method, by x-ray topography and high angular resolution x-ray diffraction. Lang topography revealed dislocations parallel and perpendicular to the crystal's surface. Double-crystal GaSb 333 x-ray topography shows dislocations and vertical stripes than can be associated with circular growth bands. We compared our high-angular resolution x-ray diffraction measurements (rocking curves) with the findings predicted by the dynamical theory of x-ray diffraction. These measurements show that our GaSb single crystals have a relative variation in the lattice parameter ({Delta}d/d) on the order of 10{sup -5}. This means that they can be used as electronic devices (detectors, for example) and as x-ray monochromators.

  14. Comparative evaluation of single crystal scintillators under x-ray imaging conditions

    Energy Technology Data Exchange (ETDEWEB)

    Valais, I G; David, S; Michail, C [Department of Medical Physics, Medical School, University of Patras, 265 00 Patras (Greece); Nomicos, C D [Department of Electronics, Technological Educational Institution of Athens, Ag. Spyridonos, Egaleo, 122 10 Athens (Greece); Panayiotakis, G S; Kandarakis, I S [Department of Medical Instruments Technology, Technological Educational Institution of Athens, Ag. Spyridonos, Egaleo, 122 10 Athens (Greece)], E-mail: kandarakis@teiath.gr

    2009-06-15

    The present study is a comparative investigation of the luminescence properties of (Lu,Y){sub 2}SiO{sub 5}: Ce (LYSO: Ce), YAlO{sub 3}: Ce (YAP: Ce), Gd{sub 2}SiO{sub 5}: Ce (GSO: Ce) and (Bi{sub 4}Ge{sub 3}O{sub 12}) BGO single crystal scintillators under x-ray excitation. Results will be of value in designing dual modality tomographic systems (PET/CT, SPECT/CT) based on a common scintillator crystal. All scintillating crystals have dimensions of 10 x 10 x 10 cm{sup 3} are non-hygroscopic exhibiting high radiation absorption efficiency in the energy range used in medical imaging applications. The comparative investigation was performed by determining the x-ray luminescence efficiency (emitted light flux over incident x-ray energy flux) in the range of x-ray energies employed in: (i) general x-ray imaging (40-140 kV, using a W/Al x-ray spectrum) and (ii) x-ray mammography imaging (22-49 kV, using a Mo/Mo x-ray spectrum). Additionally, light emission spectra of crystals at various x-ray energies were measured, in order to determine the intrinsic conversion efficiency and the spectral compatibility to optical photon detectors incorporated in medical imaging systems. The light emission performance of LYSO:Ce scintillator studied was found very high for x-ray imaging.

  15. Recombinant ACHT1 from Arabidopsis thaliana: crystallization and X-ray crystallographic analysis.

    Science.gov (United States)

    Pan, Weimin; Wang, Junchao; Yang, Ye; Liu, Lin; Zhang, Min

    2017-07-01

    Thioredoxins (Trxs) play important roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. They execute their function by regulating the oxidation and reduction of disulfide bonds. ACHT1 (atypical cysteine/histidine-rich Trx1) is a thylakoid-associated thioredoxin-type protein found in the Arabidopsis thaliana chloroplast. Recombinant ACHT1 protein was overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal diffracted to 1.7 Å resolution and a complete X-ray data set was collected. Preliminary crystallographic analysis suggested that the crystals belonged to space group C2221, with unit-cell parameters a = 102.7, b = 100.6, c = 92.8 Å.

  16. A lamellar model for the X-ray rocking curves of sagittally bent Laue crystals.

    Science.gov (United States)

    Zhong, Z; Kao, C C; Siddons, D P; Zhong, H; Hastings, J B

    2003-01-01

    The use of sagittally bent asymmetric Laue crystals in horizontally focusing monochromators for high-energy synchrotron X-rays necessitates simulation of the X-ray reflectivity by such crystals. Based on the theory of the lattice distortion in the diffraction plane of sagittally bent Laue crystals, a lamellar model was developed to predict their rocking curves. The model was experimentally verified by rocking-curve measurements from various reflections on silicon crystals of four representative orientations, sagittally bent to various radii, using X-rays of 67 keV energy.

  17. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    DEFF Research Database (Denmark)

    Yennawar, Hemant; Møller, Magda; Gillilan, Richard

    2011-01-01

    The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer...... that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies...... the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X...

  18. Antiferroelectric surface layers in a liquid crystal as observed by synchrotron x-ray scattering

    DEFF Research Database (Denmark)

    Gramsbergen, E. F.; de Jeu, W. H.; Als-Nielsen, Jens Aage

    1986-01-01

    The X-ray reflectivity form the surface of a liquid crystal with terminally polar (cyano substituted) molecules has been studied using a high-resolution triple-axis X-ray spectrometer in combination with a synchrotron source. It is demonstrated that at the surface of the smectic Al phase a few...

  19. A high resolution X-ray crystal spectrometer to study electron and ...

    Indian Academy of Sciences (India)

    We have studied fast ion–atom and electron–atom collision processes using a reconditioned high resolution X-ray spectrometer. The X-rays, generated by the collisions, are dispersed by a curved ADP crystal (Johansson geometry) and detected by a gas proportional counter. A self-written LabVIEW based program has ...

  20. Preliminary background prediction for the INTEGRAL x-ray monitor

    DEFF Research Database (Denmark)

    Feroci, M.; Costa, E.; Budtz-Joergensen, C.

    1996-01-01

    a major role. Based on the information available at the present stage of the emission design, we have computed the instrumental background to be expected because of two main background components: direct diffuse x-ray background and secondary photons originated by the interactions of the primary cosmic......The JEM-X (joint European x-ray monitor) experiment will be flown onboard the ESA's INTEGRAL satellite. The instrumental background level of the two JEM-X twin detectors will depend on several parameters, among which the satellite orbit and mass distribution, and the detectors materials play...... rays with the spacecraft structures. This calculation has been carried out by means of a Monte Carlo simulation using the code MCNP. The background due to on- orbit material activation and to the primary cosmic rays direct interactions with the detecting medium has not been considered. The INTEGRAL...

  1. Crystallization and preliminary X-ray crystallographic study of the wild type and two mutants of the CP1 hydrolytic domain from Aquifex aeolicus leucyl-tRNA synthetase

    Energy Technology Data Exchange (ETDEWEB)

    Cura, Vincent; Olieric, Natacha; Guichard, Alexandre [Département de Biologie et Génomique Structurales, UMR 7104, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Wang, En-Duo [State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031 (China); Moras, Dino [Département de Biologie et Génomique Structurales, UMR 7104, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Eriani, Gilbert [Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 Rue René Descartes, 67084 Strasbourg (France); Cavarelli, Jean, E-mail: cava@igbmc.u-strasbg.fr [Département de Biologie et Génomique Structurales, UMR 7104, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France)

    2005-10-01

    The wild-type editing CP1 domain of A. aeolicus leucyl-tRNA synthetase and two mutant CP1 domains have been overexpressed, purified and crystallized. X-ray diffraction data have been collected to 1.8 Å, which has enabled determination of the structures by molecular replacement. The editing or hydrolytic CP1 domain of leucyl-tRNA synthetase (LeuRS) hydrolyses several misactivated amino acids. The CP1 domain of Aquifex aeolicus LeuRS was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 Å. Crystals diffract to beyond 1.8 Å resolution and contain two monomers in the asymmetric unit. Two CP1 mutants in which a conserved threonine residue essential for the fidelity of the hydrolytic pathway is mutated to alanine or glutamic acid have also been expressed and crystallized. Crystals of the two CP1 mutants are isomorphs of the wild type and diffract to beyond 1.9 Å resolution. All structures were solved by molecular-replacement techniques.

  2. Instrumentations in x-ray plasma polarization spectroscopy. Crystal spectrometer, polarimeter and detectors for astronomical observations

    Energy Technology Data Exchange (ETDEWEB)

    Baronova, Elena O.; Stepanenko, Mikhail M. [RRC Kurchatov Institute, Nuclear Fusion Institute, Moscow (Russian Federation); Jakubowski, Lech [Soltan Institute for Nuclear Studies, Swierk-Otwock (Poland); Tsunemi, Hiroshi [Osaka Univ., Graduate School of Science, Osaka (Japan)

    2002-08-01

    This report discusses the various problems which are encountered when a crystal spectrometer is used for the purpose of observing polarized x-ray lines. A polarimeter is proposed based on the novel idea of using two series of equivalent atomic planes in a single crystal. The present status of the astronomical x-ray detection techniques are described with emphasis on two dimensional detectors which are polarization sensitive. (author)

  3. Biomimetic Calcium Phosphate Crystallization: Synchrotron X-ray Studies

    Science.gov (United States)

    Uysal, Ahmet; Stripe, Benjamin; Dutta, Pulak; Lin, Binhua; Meron, Mati

    2012-02-01

    The nucleation and growth of calcium phosphate by organic templates attract great attention due to its relevance to bone biomineralization. In spite of the vast studies in the field, the role of the organic templates in the process is still not well understood. One reason for this drawback is the lack of experimental tools to probe the organic template structure during the process. We studied the nucleation and growth of calcium phosphate under floating Langmuir monolayers, at the air/water interface, using two complementary X-ray scattering methods. We show that Grazing Incidence X-ray Diffraction (GID) and Grazing Incidence X-ray off-Specular Scattering (GIXOS) can reveal the organic-inorganic interface properties in situ. By using GID and GIXOS together, we can simultaneously determine the lateral interface structure and the electron density profile normal to the interface. Combined with ex situ methods, these techniques can improve our understanding of the role of the organic template during biomineralization.

  4. Characterization of single-crystal sapphire substrates by X-ray methods and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Prokhorov, I. A.; Zakharov, B. G., E-mail: zakharov@kaluga.rosmail.com [Russian Academy of Sciences, Research Center Space Materials Science, Shubnikov Institute of Crystallography (Kaluga Branch) (Russian Federation); Asadchikov, V. E.; Butashin, A. V.; Roshchin, B. S.; Tolstikhina, A. L. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Zanaveskin, M. L.; Grishchenko, Yu. V.; Muslimov, A. E. [Russian Research Center Kurchatov Institute (Russian Federation); Yakimchuk, I. V.; Volkov, Yu. O.; Kanevskii, V. M.; Tikhonov, E. O. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2011-05-15

    The possibility of characterizing a number of practically important parameters of sapphire substrates by X-ray methods is substantiated. These parameters include wafer bending, traces of an incompletely removed damaged layer that formed as a result of mechanical treatment (scratches and marks), surface roughness, damaged layer thickness, and the specific features of the substrate real structure. The features of the real structure of single-crystal sapphire substrates were investigated by nondestructive methods of double-crystal X-ray diffraction and plane-wave X-ray topography. The surface relief of the substrates was investigated by atomic force microscopy and X-ray scattering. The use of supplementing analytical methods yields the most complete information about the structural inhomogeneities and state of crystal surface, which is extremely important for optimizing the technology of substrate preparation for epitaxy.

  5. Dynamical effects in Bragg coherent x-ray diffraction imaging of finite crystals

    Science.gov (United States)

    Shabalin, A. G.; Yefanov, O. M.; Nosik, V. L.; Bushuev, V. A.; Vartanyants, I. A.

    2017-08-01

    We present simulations of Bragg coherent x-ray diffractive imaging (CXDI) data from finite crystals in the frame of the dynamical theory of x-ray diffraction. The developed approach is based on a numerical solution of modified Takagi-Taupin equations and can be applied for modeling of a broad range of x-ray diffraction experiments with finite three-dimensional crystals of arbitrary shape also in the presence of strain. We performed simulations for nanocrystals of a cubic and hemispherical shape of different sizes and provided a detailed analysis of artifacts in the Bragg CXDI reconstructions introduced by the dynamical diffraction. Based on our theoretical analysis we developed an analytical procedure to treat effects of refraction and absorption in the reconstruction. Our results elucidate limitations for the kinematical approach in the Bragg CXDI and suggest a natural criterion to distinguish between kinematical and dynamical cases in coherent x-ray diffraction on a finite crystal.

  6. Crystallization and preliminary X-ray analysis of coagulation factor IX-binding protein from habu snake venom at pH 6.5 and 4.6

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Nobuhiro [Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Shikamoto, Yasuo; Fujimoto, Zui [Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Morita, Takashi [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Mizuno, Hiroshi, E-mail: mizuno@affrc.go.jp [Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan)

    2005-01-01

    Crystals of habu coagulation factor IX-binding protein have been obtained at pH 6.5 and 4.6 and characterized by X-ray diffraction. Coagulation factor IX-binding protein isolated from Trimeresurus flavoviridis (IX-bp) is a C-type lectin-like protein. It is an anticoagulant protein consisting of homologous subunits A and B. The subunits both contain a Ca{sup 2+}-binding site with differing affinity (K{sub d} values of 14 and 130 µM at pH 7.5). These binding characteristics are pH-dependent; under acidic conditions, the affinity of the low-affinity site was reduced considerably. In order to identify which site has high affinity and also to investigate the Ca{sup 2+}-releasing mechanism, IX-bp was crystallized at pH 6.5 and 4.6. The crystals at pH 6.5 and 4.6 diffracted to 1.72 and 2.29 Å resolution, respectively; the former crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 60.7, b = 63.5, c = 66.9 Å, β = 117.0°, while the latter belong to the monoclinic space group C2, with a = 134.1, b = 37.8, c = 55.8 Å, β = 110.4°.

  7. Synthesis and Single Crystal X-Ray Crystallographic Analysis of 2 ...

    African Journals Online (AJOL)

    dihydropyrimidin-1-ium) tetrachlorocobaltate(II) [H2pymo]2[CoCl4]. The compound was re-crystallized in diethyl ether to obtain a suitable single crystal for X-ray diffraction analysis which revealed a molecule crystallizes in the orthorhombic ...

  8. X-ray microscopy of plant cells by using LiF crystal as a detector.

    Science.gov (United States)

    Reale, Lucia; Bonfigli, Francesca; Lai, Antonia; Flora, Francesco; Poma, Anna; Albertano, Patrizia; Bellezza, Simona; Montereali, Rosa Maria; Faenov, Anatoly; Pikuz, Tania; Almaviva, Salvatore; Vincenti, Maria Aurora; Francucci, Massimo; Gaudio, Pasqualino; Martellucci, Sergio; Richetta, Maria

    2008-12-01

    A lithium fluoride (LiF) crystal has been utilized as a new soft X-ray detector to image different biological samples at a high spatial resolution. This new type of image detector for X-ray microscopy has many interesting properties: high resolution (nanometer scale), permanent storage of images, the ability to clear the image and reuse the LiF crystal, and high contrast with greater dynamic range. Cells of the unicellular green algae Chlamydomonas dysosmos and Chlorella sorokiniana, and pollen grains of Olea europea have been used as biological materials for imaging. The biological samples were imaged on LiF crystals by using the soft X-ray contact microscopy and contact micro-radiography techniques. The laser plasma soft X-ray source was generated using a Nd:YAG/Glass laser focused on a solid target. The X-ray energy range for image acquisition was in the water-window spectral range for single shot contact microscopy of very thin biological samples (single cells) and around 1 keV for multishots microradiography. The main aim of this article is to highlight the possibility of using a LiF crystal as a detector for the biological imaging using soft X-ray radiation and to demonstrate its ability to visualize the microstructure within living cells. 2008 Wiley-Liss, Inc.

  9. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

  10. Crystallization and preliminary X-ray diffraction studies of the carbohydrate-recognition domain of SIGN-R1, a receptor for microbial polysaccharides and sialylated antibody on splenic marginal zone macrophages.

    Science.gov (United States)

    Silva-Martin, Noella; Schauer, Joseph D; Park, Chae Gyu; Hermoso, Juan A

    2009-12-01

    SIGN-R1, or CD209b, is a mouse C-type lectin receptor that is expressed at high levels on macrophages in lymphoid tissues, especially within the marginal zone of the spleen. SIGN-R1 can bind and mediate the uptake of various microbial polysaccharides, including dextrans, lipopolysaccharides and pneumococcal capsular polysaccharides. It has been shown that SIGN-R1 mediates the clearance of encapsulated pneumococcus, complement fixation via binding C1q independent of antibody and innate resistance to pneumococcal infection. Recently, SIGN-R1 has also been demonstrated to bind sialylated antibody and mediate its activity to suppress autoimmunity. The carbohydrate-recognition domain (CRD) of SIGN-R1 has been cloned and overexpressed in a soluble secretory form in mammalian Chinese hamster ovary (CHO) cells. The CRD protein of SIGN-R1 was purified from CHO cell-culture supernatant and concentrated for crystallization using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture of 2 M ammonium sulfate in 0.1 M bis-tris pH 5.5. Single crystals, which belonged to the monoclinic space group C2 with unit-cell parameters a = 146.72, b = 92.77, c = 77.06 A, beta = 121.66 degrees , allowed the collection of a full X-ray data set to a maximum resolution of 1.87 A.

  11. Crystallization and preliminary X-ray analysis of ginkbilobin-2 from Ginkgo biloba seeds: a novel antifungal protein with homology to the extracellular domain of plant cysteine-rich receptor-like kinases

    Energy Technology Data Exchange (ETDEWEB)

    Miyakawa, Takuya; Sawano, Yoriko; Miyazono, Ken-ichi [Department of Applied Biochemical Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Hatano, Ken-ichi [Department of Chemistry and Chemical Biology, Faculty of Engineering, Gunma University, Kiryu, Gunma 376-8515 (Japan); Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp [Department of Applied Biochemical Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2007-09-01

    Purification and crystallization of ginkbilobin-2 and its selenomethionine derivative allowed the collection of complete data to 2.38 Å resolution and multiwavelength anomalous diffraction data sets, respectively. The antifungal protein ginkbilobin-2 (Gnk2) from Ginkgo biloba seeds does not show homology to other pathogenesis-related proteins, but does show homology to the extracellular domain of plant cysteine-rich receptor-like kinases. Native Gnk2 purified from ginkgo nuts and the selenomethionine derivative of recombinant Gnk2 (SeMet-rGnk2) were crystallized by the sitting-drop vapour-diffusion method using different precipitants. X-ray diffraction data were collected from Gnk2 at 2.38 Å resolution and from SeMet-rGnk2 at 2.79 Å resolution using a synchrotron-radiation source. The crystals of both proteins belonged to the primitive cubic space group P2{sub 1}3, with unit-cell parameters a = b = c = 143.2 Å.

  12. Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction

    Science.gov (United States)

    Emamzadah, Soheila; Petty, Tom J.; De Almeida, Victor; Nishimura, Taisuke; Joly, Jacques; Ferrer, Jean-Luc; Halazonetis, Thanos D.

    2009-01-01

    Microfluidics is a promising technology for the rapid iden­tification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2 mm thin transparent cards which contain 500 chambers, each with a volume of 320 nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, including chicken lysozyme, bovine trypsin, a human p53 protein containing both the DNA-binding and oligomerization domains bound to DNA and a functionally important domain of Arabidopsis Morpheus’ molecule 1 (MOM1). The latter two polypeptides have not been crystallized previously. For X-ray diffraction analysis, either the cards were opened to allow mounting of the crystals on loops or the crystals were exposed to X-rays in situ. For lysozyme, an entire X-ray diffraction data set at 1.5 Å resolution was collected without removing the crystal from the card. Thus, cyclic olefin homopolymer-based microfluidics systems have the potential to further automate protein crystallization and structural genomics efforts. PMID:19690369

  13. A versatile, highly-efficient, high-resolution von Hamos Bragg crystal x-ray spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Vane, C.R.; Smith, M.S.; Raman, S.

    1988-01-01

    An efficient, high-resolution, vertical-focusing, Bragg crystal x-ray spectrometer has been specifically designed and constructed for use in measurements of x rays produced in collisions of energetic heavy ions. In this report the design and resulting operational characteristics of the final instrument are fully described. A wide variety of sample data is also included to illustrate the utility of this device in several areas of research. 14 refs., 38 figs.

  14. Nanosecond X-ray detector based on high resistivity ZnO single crystal semiconductor

    Science.gov (United States)

    Zhao, Xiaolong; Chen, Liang; He, Yongning; Liu, Jinliang; Peng, Wenbo; Huang, Zhiyong; Qi, Xiaomeng; Pan, Zijian; Zhang, Wenting; Zhang, Zhongbing; Ouyang, Xiaoping

    2016-04-01

    The pulse radiation detectors are sorely needed in the fields of nuclear reaction monitoring, material analysis, astronomy study, spacecraft navigation, and space communication. In this work, we demonstrate a nanosecond X-ray detector based on ZnO single crystal semiconductor, which emerges as a promising compound-semiconductor radiation detection material for its high radiation tolerance and advanced large-size bulk crystal growth technique. The resistivity of the ZnO single crystal is as high as 1013 Ω cm due to the compensation of the donor defects (VO) and acceptor defects (VZn and Oi) after high temperature annealing in oxygen. The photoconductive X-ray detector was fabricated using the high resistivity ZnO single crystal. The rise time and fall time of the detector to a 10 ps pulse electron beam are 0.8 ns and 3.3 ns, respectively, indicating great potential for ultrafast X-ray detection applications.

  15. Expression, purification and preliminary X-ray diffraction studies of the transcriptional factor PyrR from Bacillus halodurans

    Energy Technology Data Exchange (ETDEWEB)

    Arreola, Rodrigo [Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510 (Mexico); Vega-Miranda, Anita [Instituto Nacional de Enfermedades Respiratorias, Calzada de Tlalpan 4502, México DF 14080 (Mexico); Gómez-Puyou, Armando; Pérez-Montfort, Ruy [Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510 (Mexico); Merino-Pérez, Enrique [Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, Morelos (Mexico); Torres-Larios, Alfredo, E-mail: torres@ifc.unam.mx [Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510 (Mexico)

    2008-08-01

    The gene-regulation factor PyrR from B. halodurans has been crystallized in two crystal forms. Preliminary crystallographic analysis showed that the protein forms tetramers in both space groups. The PyrR transcriptional regulator is widely distributed in bacteria. This RNA-binding protein is involved in the control of genes involved in pyrimidine biosynthesis, in which uridyl and guanyl nucleotides function as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of two crystal forms of Bacillus halodurans PyrR are reported. One of the forms belongs to the monoclinic space group P2{sub 1} with unit-cell parameters a = 59.7, b = 87.4, c = 72.1 Å, β = 104.4°, while the other form belongs to the orthorhombic space group P22{sub 1}2{sub 1} with unit-cell parameters a = 72.7, b = 95.9, c = 177.1 Å. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of four and six monomers per asymmetric unit; a crystallographic tetramer is formed in both forms.

  16. Performance of the x-ray free-electron laser oscillator with crystal cavity

    OpenAIRE

    R. R. Lindberg; K.-J. Kim; Yu. Shvyd’ko; W. M. Fawley

    2011-01-01

    Simulations of the x-ray free-electron laser (FEL) oscillator are presented that include the frequency-dependent Bragg crystal reflectivity and the transverse diffraction and focusing using the two-dimensional FEL code GINGER. A review of the physics of Bragg crystal reflectors and the x-ray FEL oscillator is made, followed by a discussion of its numerical implementation in GINGER. The simulation results for a two-crystal cavity and realistic FEL parameters indicate ∼10^{9} photons in a nearl...

  17. Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Armour, Wes [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Oxford e-Research Centre, 7 Keble Road, Oxford OX1 3QG (United Kingdom); Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Horrell, Sam [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); University of Liverpool, Liverpool L69 3BX (United Kingdom); McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2013-07-01

    A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

  18. Protein crystal structure from non-oriented, single-axis sparse X-ray data

    Directory of Open Access Journals (Sweden)

    Jennifer L. Wierman

    2016-01-01

    Full Text Available X-ray free-electron lasers (XFELs have inspired the development of serial femtosecond crystallography (SFX as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ∼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases

  19. Protein crystal structure from non-oriented, single-axis sparse X-ray data.

    Science.gov (United States)

    Wierman, Jennifer L; Lan, Ti-Yen; Tate, Mark W; Philipp, Hugh T; Elser, Veit; Gruner, Sol M

    2016-01-01

    X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so 'sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ∼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are

  20. Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Emamzadah, Soheila [Department of Molecular Biology, University of Geneva, CH-1205 Geneva (Switzerland); Department of Biochemistry, University of Geneva, CH-1205 Geneva (Switzerland); Petty, Tom J. [Department of Molecular Biology, University of Geneva, CH-1205 Geneva (Switzerland); Biomedical Graduate Studies Genomics and Computational Biology Group, University of Pennsylvania, Philadelphia, PA 19104 (United States); De Almeida, Victor [Department of Molecular Biology, University of Geneva, CH-1205 Geneva (Switzerland); Department of Biochemistry, University of Geneva, CH-1205 Geneva (Switzerland); Nishimura, Taisuke [Department of Plant Biology, University of Geneva, CH-1205 Geneva (Switzerland); Joly, Jacques; Ferrer, Jean-Luc [Institut de Biologie Structurale J.-P. Ebel, CEA-CNRS-University J. Fourier, 38027 Grenoble CEDEX 1 (France); Halazonetis, Thanos D., E-mail: thanos.halazonetis@unige.ch [Department of Molecular Biology, University of Geneva, CH-1205 Geneva (Switzerland); Department of Biochemistry, University of Geneva, CH-1205 Geneva (Switzerland)

    2009-09-01

    A cyclic olefin homopolymer-based microfluidics system has been established for protein crystallization and in situ X-ray diffraction. Microfluidics is a promising technology for the rapid identification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2 mm thin transparent cards which contain 500 chambers, each with a volume of 320 nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, including chicken lysozyme, bovine trypsin, a human p53 protein containing both the DNA-binding and oligomerization domains bound to DNA and a functionally important domain of Arabidopsis Morpheus’ molecule 1 (MOM1). The latter two polypeptides have not been crystallized previously. For X-ray diffraction analysis, either the cards were opened to allow mounting of the crystals on loops or the crystals were exposed to X-rays in situ. For lysozyme, an entire X-ray diffraction data set at 1.5 Å resolution was collected without removing the crystal from the card. Thus, cyclic olefin homopolymer-based microfluidics systems have the potential to further automate protein crystallization and structural genomics efforts.

  1. Self-standing quasi-mosaic crystals for focusing hard X-rays

    Science.gov (United States)

    Camattari, Riccardo; Guidi, Vincenzo; Bellucci, Valerio; Neri, Ilaria; Frontera, Filippo; Jentschel, Michael

    2013-05-01

    A quasi mosaic bent crystal for high-resolution diffraction of X and γ rays has been realized. A net curvature was imprinted to the crystal thanks to a series of superficial grooves to keep the curvature without external devices. The crystal highlights very high diffraction efficiency due to quasi mosaic curvature. Quasi mosaic crystals of this kind are proposed for the realization of a high-resolution focusing Laue lens for hard X-rays.

  2. Development of an X-ray fluorescence holographic measurement system for protein crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sato-Tomita, Ayana, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Shibayama, Naoya, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Okabe, Takahiro [Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke 329-0498 (Japan); Happo, Naohisa [Department of Computer and Network Engineering, Graduate School of Information Sciences, Hiroshima City University, Asa-Minami-Ku, Hiroshima 731-3194 (Japan); Kimura, Koji [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Matsushita, Tomohiro [Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Sayo, Hyogo 679-5198 (Japan); Park, Sam-Yong [Drug Design Laboratory, Department of Medical Life Science, Yokohama City University, Suehiro, Tsurumi, Yokohama 230-0045 (Japan); Sasaki, Yuji C. [Department of Advanced Material Science, Graduate School of Frontier Science, The University of Tokyo, Kashiwanoha, Kashiwa 277-8561 (Japan); Hayashi, Kouichi, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan)

    2016-06-15

    Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α{sub 2}β{sub 2} tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm{sup 3}) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

  3. Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; Kick, Leonhard M.; Gati, Cornelius; Nelson, Garrett; Deupi, Xavier; Standfuss, Jörg; Schertler, Gebhard; Panneels, Valérie, E-mail: valerie.panneels@psi.ch [Paul Scherrer Institute, OFLC/103, 5232 Villigen-PSI (Switzerland)

    2015-06-27

    A new batch preparation method is presented for high-density micrometre-sized crystals of the G protein-coupled receptor rhodopsin for use in time-resolved serial femtosecond crystallography at an X-ray free-electron laser using a liquid jet. Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallization conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.

  4. Double-slit dynamical diffraction of X-rays in ideal crystals (Laue case).

    Science.gov (United States)

    Balyan, Minas K

    2010-11-01

    The theoretical investigation of double-slit dynamical X-ray diffraction in ideal crystals shows that, on the exit surface of crystals, interference fringes similar to Young's fringes are formed. An expression for the period of the fringes was obtained. The visibility of the fringes depending on temporal and spatial coherent properties of the incident beam is studied. The polarization state of the incident beam also affects the visibility of the fringes, which in turn depends on the size of the slits. The deviation from Bragg's exact angle causes a shift of the fringes and can also affect the amplitude of the intensity. One of the parameters on which the visibility of the fringes depends is the source-crystal distance. The proposed scheme can be used as a Rayleigh X-ray interferometer. Use of the scheme as a Michelson X-ray stellar interferometer is also possible.

  5. Preliminary results from the 'HXR' hard X-ray sky survey

    Energy Technology Data Exchange (ETDEWEB)

    Ubertini, P.; Bazzano, A.; LaPadula, C.; Polcaro, V.F.; Zambon, G. (Consiglio Nazionale delle Ricerche, Frascati (Italy). Lab. di Astrofisica Spaziale); Manchanda, R.K. (Tata Inst. of Fundamental Research, Bombay (India))

    1984-01-01

    The authors present the preliminary results of the HXR81M experiment: a one square meter hard X-ray balloon-borne telescope. The detected excesses on 14 sources are given in catalogue form and the spectra, reduced at the top of the atmosphere, of a number of galactic and extragalactic sources are shortly discussed.

  6. Synchrotron X-ray diffraction imaging studies of dislocations in Kyropoulos grown Ti doped sapphire crystal

    Science.gov (United States)

    Sen, Gourav; Tran Caliste, Thu Nhi; Stelian, Carmen; Baruchel, José; Barthalay, Nicolas; Duffar, Thierry

    2017-06-01

    In this study, X-ray diffraction and X-ray topography, using synchrotron radiation source, were used to analyse the nature of defects in a sapphire single crystal sample grown by Kyropoulos method. Qualitative and quantitative analysis were carried out on the results of the topography experiments. The dislocation density was found to be around 103-104 dislocations/cm2 indicating a crystal of good crystalline quality. Also, the variation of dislocation density with respect to the position on the sample was observed and discussed.

  7. Synthesis and single crystal X-ray analysis of two griseofulvin metabolites

    DEFF Research Database (Denmark)

    Rønnest, Mads Holger; Harris, Pernille; Gotfredsen, Charlotte Held

    2010-01-01

    The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis.......The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis....

  8. Crystallization kinetics of amorphous griseofulvin by pattern fitting procedure using X-ray diffraction data.

    Science.gov (United States)

    Yamamura, Shigeo; Takahira, Rieko; Momose, Yasunori

    2007-05-01

    A pattern fitting procedure using X-ray powder diffraction patterns was applied to study the crystallization kinetics of amorphous griseofulvin. From the optimized parameters obtained by pattern fitting, a change in the quantity and quality of griseofulvin crystals with crystallization was also investigated. Amorphous griseofulvin was prepared by cooling the melts followed by pulverization. X-ray diffraction patterns of amorphous griseofulvin were repeatedly measured every 20 h. The observed pattern was separated into crystalline diffraction intensity and amorphous scattering intensity by the nonlinear least-squares procedure. The fitting between the observed and simulated diffraction patterns was satisfactorily independent of the degree of crystallinity. Since a good linear relationship was found in a plot of amorphous scattering intensity against crystalline diffraction intensity, the degree of crystallinity can be determined according to Hermans' method. The diffraction peak width increased with higher diffraction angles with crystallization. The crystallization was biphasic: fast and slow crystallization with the growth of low disordered crystals and disordered crystals, respectively. The pattern fitting procedure is a powerful tool to analyze the X-ray diffraction patterns of semicrystalline materials. This procedure can simultaneously analyze the degree of crystallinity and crystal disorder in semicrystalline samples during crystallization.

  9. Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystals.

    Science.gov (United States)

    Haugh, M J; Wu, M; Jacoby, K D; Loisel, G P

    2014-11-01

    This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals that we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories in Albuquerque, New Mexico. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a double crystal diffractometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.

  10. First indirect x-ray imaging tests with an 88-mm diameter single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A. H. [Fermilab; Macrander, A. T. [Argonne

    2017-02-01

    Using the 1-BM-C beamline at the Advanced Photon Source (APS), we have performed the initial indirect x - ray imaging point-spread-function (PSF) test of a unique 88-mm diameter YAG:Ce single crystal of only 100 - micron thickness. The crystal was bonded to a fiber optic plat e (FOP) for mechanical support and to allow the option for FO coupling to a large format camera. This configuration resolution was compared to that of self - supported 25-mm diameter crystals, with and without an Al reflective coating. An upstream monochromator was used to select 17-keV x-rays from the broadband APS bending magnet source of synchrotron radiation. The upstream , adjustable Mo collimators were then used to provide a series of x-ray source transverse sizes from 200 microns down to about 15-20 microns (FWHM) at the crystal surface. The emitted scintillator radiation was in this case lens coupled to the ANDOR Neo sCMOS camera, and the indirect x-ray images were processed offline by a MATLAB - based image processing program. Based on single Gaussian peak fits to the x-ray image projected profiles, we observed a 10.5 micron PSF. This sample thus exhibited superior spatial resolution to standard P43 polycrystalline phosphors of the same thickness which would have about a 100-micron PSF. Lastly, this single crystal resolution combined with the 88-mm diameter makes it a candidate to support future x-ray diffraction or wafer topography experiments.

  11. Simultaneous X-ray diffraction from multiple single crystals of macromolecules

    DEFF Research Database (Denmark)

    Paithankar, Karthik S.; Sørensen, Henning Osholm; Wright, Jonathan P.

    2011-01-01

    The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedu...... could be useful both in relation to diffraction data obtained from intergrown crystals and to alleviate the problem of rapid diffraction decay arising from the effects of radiation damage....

  12. Controllable reflection of X-rays on crystals of saccharose

    CERN Document Server

    Navasardyan, M A; Hayrapetyan, K T; Gabrielyan, R T

    2003-01-01

    Multiple (ten times and more) increase in intensities of separate reflections and of lauegram reflections from organic single crystals of saccharose (C sub 1 2H sub 2 2O sub 1 1) was observed under influence of certain temperature gradient. On the base of the present experiment and the data of our previous woks we show that the controllable reflection process has a common nature and the intensity of the diffracted beam under external influences does not depend on the total number of electrons per unit volume of the unit cell of the single crystal.

  13. High Miller-index germanium crystals for high-energy x-ray imaging applications.

    Science.gov (United States)

    Koch, J A; Lee, J J; Haugh, M J

    2015-12-01

    Near-normal-incidence bent crystals are widely used for x-ray imaging applications. Advantages include high collection solid angle and potentially high efficiency for narrow-band sources, while disadvantages include relatively large (several Å) interatomic spacings and a limited number of suitable matches between a crystal 2d value and an integral multiple of useful emission line wavelengths. The disadvantages become more significant at x-ray energies >10  keV. The former disadvantage can be mitigated by using high-order reflections from crystal planes having low Miller indices, but both disadvantages can be mitigated by using low-order reflections from crystal planes having high Miller indices. We report here on integrated reflectivity measurements we performed of Ge (15,7,7) (2d=0.6296  Å), a candidate for imaging Ru He-α (θ(B)=87°). We find good agreement with calculations, and the data show a multitude of closely spaced reflections with slightly different Bragg angles including a fifth-order reflection of Ge (3,1,1) that has comparable reflectivity. This demonstrates that arbitrary choices of Miller indices in Ge crystals can be used to fine-tune Bragg angles for near-normal-incidence x-ray imaging at tens of kiloelectron volt x-ray energies with minimal lower-energy contamination from lower-order reflections, and that existing calculational tools can be used to reliably estimate integrated reflectivity.

  14. Femtosecond X-ray diffraction from two-dimensional protein crystals

    Directory of Open Access Journals (Sweden)

    Matthias Frank

    2014-03-01

    Full Text Available X-ray diffraction patterns from two-dimensional (2-D protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  15. Crystallization and X-ray diffraction data of Thermus flavus 5S rRNA helices

    Science.gov (United States)

    Vallazza, Marco; Senge, Andrea; Lippmann, Corinna; Perbandt, Markus; Betzel, Christian; Bald, Rolf; Erdmann, Volker A.

    2001-11-01

    5S rRNA is an essential component of the large ribosomal subunit in prokaryotes and eukaryotes. Its unknown function in the ribosome will eventually be revealed in part by structural studies. To promote crystallization and enhance resolution in X-ray diffraction the molecule was subdivided into five domains A-E. Several RNA oligonucleotides were chemically produced by solid-phase phosphoramidite synthesis in order to construct the domains of the 5S rRNA. An improved RNA-MPD-screen was applied in crystallization which covers a complete 2D matrix for the components used. Crystallization analysis resulted in preferred combinations of pH, polyamine, monovalent and divalent cations for short RNA molecules. Six types of crystals corresponding to the domains B, C and E of Thermus flavus 5S rRNA could be obtained which were suitable for X-ray diffraction. Four RNA helices consist of seven base pairs and two of eight base pairs. As special features, they contain two adenines in a bulge position or G : U wobble base pairs assumed to be involved in RNA-protein recognition. With an increase in crystal size an increase in resolution by X-ray analysis was observed. X-ray diffraction data were collected to 1.5 Å resolution using synchrotron radiation and cryogenic cooling techniques.

  16. Preliminary assessment of the ATHENA/WFI non-X-ray background

    Science.gov (United States)

    Perinati, Emanuele; Barbera, Marco; Diebold, Sebastian; Guzman, Alejandro; Santangelo, Andrea; Tenzer, Chris

    2017-12-01

    We present a preliminary assessment of the non-X-ray background for the WFI on board ATHENA conducted at IAAT in the context of the collaborative background and radiation damage working group activities. Our main result is that in the baseline configuration originally assumed for the camera the requirement on the level of non-X-ray background could not be met. In light of the results of Geant4 simulations we propose and discuss a possible optimization of the camera design and pinpoint some open issues to be addressed in the next phase of investigation. One of these concerns the possible contribution to the non-X-ray background from soft protons and ions funneled to the focal plane through the optics. This is not quantified at this stage, here we just briefly report on our ongoing activities aimed at validating the mechanisms of proton scattering at grazing incidence.

  17. Preliminary investigation of changes in x-ray multilayer optics subjected to high radiation flux

    Energy Technology Data Exchange (ETDEWEB)

    Hockaday, M.P.; Blake, R.L.; Grosso, J.S.; Selph, M.M.; Klein, M.M.; Matuska, W. Jr.; Palmer, M.A.; Liefeld, R.J.

    1985-01-01

    A variety of metal multilayers was exposed to high x-ray flux using Sandia National Laboratories' PROTO II machine in the gas puff mode. Fluxes incident on the multilayers above 700 MW/cm/sup 2/ in total radiation, in nominal 20 ns pulses, were realized. The neon hydrogen- and helium-like resonance lines were used to probe the x-ray reflectivity properties of the multilayers as they underwent change of state during the heating pulse. A fluorescer-fiber optic-streak camera system was used to monitor the changes in x-ray reflectivity as a function of time and irradiance. Preliminary results are presented for a W/C multilayer. Work in progress to model the experiment is discussed. 13 refs., 4 figs.

  18. Correct interpretation of diffraction properties of quartz crystals for X-ray optics applications

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Xian-Rong; Gog, Thomas; Kim, Jungho; Kasman, Elina; Said, Ayman H.; Casa, Diego M.; Wieczorek, Michael; Hönnicke, Marcelo G.; Assoufid, Lahsen

    2018-02-01

    Quartz has hundreds of strong Bragg reflections that may offer a great number of choices for making fixed-angle X-ray analyzers and polarizers at virtually any hard X-ray energies with selectable resolution. However, quartz crystals, unlike silicon and germanium, are chiral and may thus appear in two different forms of handedness that are mirror images. Furthermore, because of the threefold rotational symmetry along thecaxis, the {h1h2h3L} and {h2h1h3L} Bragg reflections may have quite different Darwin bandwidth, reflectivity and angular acceptance, although they have the same Bragg angle. The design of X-ray optics from quartz crystals therefore requires unambiguous determination of the orientation, handedness and polarity of the crystals. The Laue method and single-axis diffraction technique can provide such information, but the variety of conventions used in the literature to describe quartz structures has caused widespread confusion. The current studies give detailed guidelines for design and fabrication of quartz X-ray optics, with special emphasis on the correct interpretation of Laue patterns in terms of the crystallography and diffraction properties of quartz. Meanwhile, the quartz crystals examined were confirmed by X-ray topography to have acceptably low densities of dislocations and other defects, which is the foundation for developing high-resolution quartz-based X-ray optics.

  19. Cloning, purification and preliminary X-ray analysis of the C-terminal domain of Helicobacter pylori MotB

    Energy Technology Data Exchange (ETDEWEB)

    Roujeinikova, Anna, E-mail: anna.roujeinikova@manchester.ac.uk [Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom)

    2008-04-01

    The cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of a putative peptidoglycan-binding domain of H. pylori MotB, a stator component of the bacterial flagellar motor, are reported. The C-terminal domain of MotB (MotB-C) contains a putative peptidoglycan-binding motif and is believed to anchor the MotA/MotB stator unit of the bacterial flagellar motor to the cell wall. Crystals of Helicobacter pylori MotB-C (138 amino-acid residues) were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. These crystals belong to space group P2{sub 1}, with unit-cell parameters a = 50.8, b = 89.5, c = 66.3 Å, β = 112.5°. The crystals diffract X-rays to at least 1.6 Å resolution using a synchrotron-radiation source. Self-rotation function and Matthews coefficient calculations suggest that the asymmetric unit contains one tetramer with 222 point-group symmetry. The anomalous difference Patterson maps calculated for an ytterbium-derivative crystal using diffraction data at a wavelength of 1.38 Å showed significant peaks on the v = 1/2 Harker section, suggesting that ab initio phase information could be derived from the MAD data.

  20. Parametric X-ray radiation in crystals theory, experiments and applications

    CERN Document Server

    Baryshevsky, Vladimir G; Ulyanenkov, Alexander P

    2005-01-01

    This systematic and comprehensive monograph is devoted to parametric X-ray radiation (PXR). This radiation is generated by the motion of electrons inside a crystal, whereby the emitted photons are diffracted by the crystal and the radiation intensity critically depends on the parameters of the crystal structure. Nowadays PXR is the subject of numerous theoretical and experimental studies throughout the world. The first part of the book is a theoretical treatment of PXR, which includes a new approach to describe the radiation process in crystals. The second part is a survey of PXR experimental results and the possible applications of PXR as a tool for crystal structure analysis and a source of tunable X-ray radiation.

  1. Development of an x-ray detector based on polymer- dispersed liquid crystal

    Science.gov (United States)

    Oh, K.; Hong, J.; Kim, G.; Park, S.; Min, B.; Yang, J.; Nam, S.

    2015-02-01

    The applications of active matrix flat-panel imagers (AMFPIs) in large-area x-ray imaging systems have increased over time but are still severely limited owing to its pixel resolution, complex fabrication processes, and high cost. As a solution, x-ray light valve (XLV) technology was introduced and expected to have a better resolution and contrast ratio than those of AMFPI, owing to its micrometer level of the LC cells and signal amplification by an external light source. The twisting angle of the LC cells was changed by charge carrier signals created in a photoconductor layer against x-rays, and the diagnostic images from XLV were acquired from the transmittance of the external light source. However, there was a possibility that the photoconductor layer may be crystallized or degenerated due to the application of high temperatures for sealing the LC layer during the fabrication process. To solve such problems, polymer-dispersed liquid crystals (PDLCs), which do not need high temperature for the sealing process of the LC layer, are used in this study instead of typical LC cells. A photoconductor and PDLC are combined to develop an x-ray detector. An external light source and optical sensor are used to investigate the light transmission of the PDLC . The PDLCs used in this paper do not need polarizers and are self-adhesive. Hence, the transmittance is very high in the transparent state, which allows for a linear x-ray response and sufficient dynamic range in digital radiography.

  2. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals.

    Science.gov (United States)

    Dao, E Han; Sierra, Raymond G; Laksmono, Hartawan; Lemke, Henrik T; Alonso-Mori, Roberto; Coey, Aaron; Larsen, Kevin; Baxter, Elizabeth L; Cohen, Aina E; Soltis, S Michael; DeMirci, Hasan

    2015-07-01

    In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.

  3. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

    Directory of Open Access Journals (Sweden)

    E. Han Dao

    2015-07-01

    Full Text Available In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.

  4. High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

    Science.gov (United States)

    Smither, Robert K [Hinsdale, IL

    2011-05-17

    A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

  5. Flexible X-ray detector based on sliced lead iodide crystal

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hui; Gao, Xiuying [College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu (China); Department of Materials Science, Sichuan University, Chengdu (China); Zhao, Beijun [Department of Materials Science, Sichuan University, Chengdu (China); Yang, Dingyu; Wangyang, Peihua; Zhu, Xinghua [College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu (China)

    2017-02-15

    A promising flexible X-ray detector based on inorganic semiconductor PbI{sub 2} crystal is reported. The sliced crystals mechanically cleaved from an as-grown PbI{sub 2} crystal act as the absorber directly converting the impinging X-ray photons to electron hole pairs. Due to the ductile feature of the PbI{sub 2} crystal, the detector can be operated under a highly curved state with the strain on the top surface up to 1.03% and still maintaining effective detection performance. The stable photocurrent and fast response were obtained with the detector repeated bending to a strain of 1.03% for 100 cycles. This work presents an approach for developing efficient and cost-effective PbI{sub 2}-based flexible X-ray detector. Photocurrent responses of the flexible PbI{sub 2} X-ray detector with the strain on the top surface up to 1.03% proposed in this work with the cross sectional structure and curved detector photograph as insets. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Microcontroller-based servo for two-crystal X-ray monochromators.

    Science.gov (United States)

    Siddons, D P

    1998-05-01

    Microcontrollers have become increasingly easy to incorporate into instruments as the architectures and support tools have developed. The PIC series is particularly easy to use, and this paper describes a controller used to stabilize the output of a two-crystal X-ray monochromator at a given offset from its peak intensity position, as such monochromators are generally used.

  7. Doubly curved imaging Bragg crystal spectrometer for X-ray astronomy

    DEFF Research Database (Denmark)

    Byrnak, B. P.; Christensen, Finn Erland; Westergaard, Niels Jørgen Stenfeldt

    1985-01-01

    An X-ray spectrometer which is sensitive in the 0.5-7-keV energy range and is intended for use onboard astronomical satellites has been studied. The Bragg reflected rays from a doubly bent crystal positioned downstream of the focal plane of a grazing-incidence concentrator are focused along the a...

  8. X-ray absorption spectroscopy of PbMoO 4 single crystals

    Indian Academy of Sciences (India)

    X-ray absorption spectra of PbMoO4 (LMO) crystals have been investigated for the first time in literature. The measurements have been carried out at Mo absorption edge at the dispersive EXAFS beamline (BL-8) of INDUS-2 Synchrotron facility at Indore, India. The optics of the beamline was set to obtain a band of 2000 eV ...

  9. A = Rb, K: Single crystal X-ray diffraction studies

    Indian Academy of Sciences (India)

    Unknown

    Abstract. The crystal structure of ferroelastic Rb4Li(HSO4)3(SO4) has been deter- mined at two temperatures, which indicates a structural phase transition, tetragonal. P43 with a = 7⋅629(1) Е , c = 29⋅497(2) Е at 293 K and monoclinic P21 with a = 7⋅583(3) Е , b = 29⋅230(19) Е , c = 7⋅536(5) Е , β = 90⋅14(1)° at 90 K.

  10. Convex Crystal X-ray Spectrometer for Laser Plasma Experiments

    Energy Technology Data Exchange (ETDEWEB)

    May, M; Heeter, R; Emig, J

    2004-04-15

    Measuring time and space-resolved spectra is important for understanding Hohlraum and Halfraum plasmas. Experiments at the OMEGA laser have used the Nova TSPEC which was not optimized for the OMEGA diagnostic space envelope or for the needed spectroscopic coverage and resolution. An improved multipurpose spectrometer snout, the MSPEC, has been constructed and fielded on OMEGA. The MSPEC provides the maximal internal volume for mounting crystals without any beam interferences at either 2x or 3x magnification. The RAP crystal is in a convex mounting geometry bent to a 20 cm radius of curvature. The spectral resolution, E/dE, is about 200 at 2.5 keV. The spectral coverage is 2 to 4.5 keV. The MSPEC can record four separate spectra on the framing camera at time intervals of up to several ns. The spectrometer design and initial field-test performance will be presented and compared to that of the TSPEC. Work supported by U. S. DoE/UC LLNL contract W-7405-ENG-48

  11. Mosaic GaAs crystals for hard x-ray astronomy

    Science.gov (United States)

    Ferrari, C.; Zanotti, L.; Zappettini, A.; Arumainathan, S.

    2008-08-01

    Recently the design of a Laue lens with field of view of 30 arcseconds and for x-rays in the energy range from 100 keV to 1 MeV has been proposed in which mosaic crystals are used as focussing elements. The proper mosaic angular spread is chosen as a compromise between intensity and energy resolution of the Laue lens. In the present work we consider the use of GaAs crystals as optical elements for hard x-ray astronomy. GaAs crystals have essentially the same electron density and lattice spacing as germanium, and are characterized by spontaneous formation of "cellular structures" with dislocations distribution at the boundaries between perfect zones of the crystal. Because of the presence of cellular structures Czochralsky grown GaAs show a natural degree of mosaicity. Several GaAs ingots grown by liquid encapsulating Czochralsky technique have been characterized by high resolution x-ray diffraction. Bragg diffraction profiles have been measured along ingot axes and diameters of doped, undoped or stoichiometry deviated GaAs crystals. Full width at half maximum values ranging from 15 to 40 arcseconds depending on the position were measured close to the proposed 30 arcsecond mosaicity required for the Laue lens. Appropriate growth conditions allow the control of the dislocation density and the modification of cellular structure responsible of the crystal mosaicity so that the possibility of obtaining crystals with a given degree of mosaicity by tuning the LEC growth conditions is proposed.

  12. Focusing characteristics of diamond crystal x-ray monochromators. An experimental and theoretical comparison

    DEFF Research Database (Denmark)

    Rio, M.S. del; Grübel, G.; Als-Nielsen, J.

    1995-01-01

    Perfect crystals in transmission (Laue) geometry can be used effectively for x-ray monochromators, and moreover, perfect Laue crystals show an interesting focusing effect when the incident beam is white and divergent. This focusing is directly dependent on the incident beam divergence...... and on the diffraction profile width of the crystal. The aim of this work is to study whether this property can be used for focusing a synchrotron x-ray beam, and to obtain quantitatively the dimensions of the resulting monochromatic beam. We have experimentally measured the size of an undulator beam after diffraction...... from a diamond crystal in Lane geometry, and we analyze and explain the results by comparison with ray-tracing simulations. (C) 1995 American Institute of Physics....

  13. Integrated x-ray reflectivity measurements of elliptically curved pentaerythritol crystals.

    Science.gov (United States)

    Haugh, M J; Regan, S P; Jacoby, K D; Ross, P W; Magoon, J; Barrios, M A; Emig, J A; Shoup, M J; Fournier, K B

    2012-10-01

    The elliptically curved pentaerythritol (PET) crystals used in the Supersnout 2 x-ray spectrometer on the National Ignition Facility at Lawrence Livermore National Laboratory have been calibrated photometrically in the range of 5.5-16 keV. The elliptical geometry provides broad spectral coverage and minimizes the degradation of spectral resolution due to the finite source size. The reflectivity curve of the crystals was measured using a x-ray line source. The integrated reflectivity (R(I)) and width of its curve (ΔΘ) were the measurements of major interest. The former gives the spectrometer throughput, and the latter gives the spectrometer resolving power. Both parameters are found to vary considerably with the radius of curvature of the crystal and with spectral energy. The results are attributed to an enhanced mosaic effect due to the increase in curvature. There are also contributions from the crystal cleaving and gluing processes.

  14. Artificial Temperature Anisotropy of Crystals in X-Ray Frequency Range

    Science.gov (United States)

    Mkrtchyan, Vahram P.; Gasparyan, Laura G.; Balyan, Minas K.

    2010-04-01

    The effect of artificial temperature anisotropy of crystals in X-ray frequency range was observed for the first time and an effort to theoretically interpret this effect in Bragg-Laue diffraction case was made. It was established that an isotropic crystal optically turns into an artificially anisotropic one with optical axis along the direction of applied external influence as a symmetry axis, giving rise to the double refraction.

  15. Dynamic crystal rotation resolved by high-speed synchrotron X-ray Laue diffraction

    OpenAIRE

    Huang, J.W.; E, J. C.; Huang, J. Y.; Sun, T.; Fezzaa, K.; Luo, S.N.

    2016-01-01

    Dynamic compression experiments are performed on single-crystal Si under split Hopkinson pressure bar loading, together with simultaneous high-speed (250?350?ns resolution) synchrotron X-ray Laue diffraction and phase-contrast imaging. A methodology is presented which determines crystal rotation parameters, i.e. instantaneous rotation axes and angles, from two unindexed Laue diffraction spots. Two-dimensional translation is obtained from dynamic imaging by a single camera. High-speed motion o...

  16. Angle-resolved x-ray imaging using a resolution-tunable double-crystal analyser

    CERN Document Server

    Hirano, K

    2003-01-01

    A resolution-tunable double-crystal analyser was successfully applied, for the first time, to angle-resolved x-ray imaging. Tuning the resolution between 0.5'' and 2.3'' was done with small loss of peak intensity using a Si(220) double-crystal analyser. The angle-resolved images of a housefly were recorded on nuclear emulsion plates at various angular resolutions. Several methods to improve the angular resolution of the analyser are also proposed.

  17. Purification, crystallization and X-ray diffraction analysis of human synaptotagmin 1 C2A-C2B

    Energy Technology Data Exchange (ETDEWEB)

    Montes, Miguel [Department of Neuroscience and Cell Biology, The University of Texas Medical Branch, Galveston, TX 77555-0437 (United States); Fuson, Kerry L. [Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555-0437 (United States); Sutton, R. Bryan, E-mail: rbsutton@utmb.edu [Department of Neuroscience and Cell Biology, The University of Texas Medical Branch, Galveston, TX 77555-0437 (United States); Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555-0437 (United States); Robert, J. Justin [Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555-0437 (United States); Department of Neuroscience and Cell Biology, The University of Texas Medical Branch, Galveston, TX 77555-0437 (United States)

    2006-09-01

    Human synaptotagmin C2A-C2B has been expressed as a glutathione-S-transferase fusion protein in Escherichia coli. The purification, crystallization and preliminary X-ray analysis of this protein are reported here. Synaptotagmin acts as the Ca{sup 2+} sensor for neuronal exocytosis. The cytosolic domain of human synaptotagmin 1 is composed of tandem C2 domains: C2A and C2B. These C2 domains modulate the interaction of synaptotagmin with the phospholipid bilayer of the presynaptic terminus and effector proteins such as the SNARE complex. Human synaptotagmin C2A-C2B has been expressed as a glutathione-S-transferase fusion protein in Escherichia coli. The purification, crystallization and preliminary X-ray analysis of this protein are reported here. The crystals diffract to 2.7 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 82.37, b = 86.31, c = 140.2 Å. From self-rotation function analysis, there are two molecules in the asymmetric unit. The structure determination of the protein using this data is ongoing.

  18. Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

    Science.gov (United States)

    Warren, Anna J; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R; Horrell, Sam; McAuley, Katherine E; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

    2013-07-01

    The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

  19. Single crystal X-ray structure of the artists’ pigment zinc yellow

    DEFF Research Database (Denmark)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold

    2017-01-01

    The artists’ pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto...... been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning...... electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography...

  20. Increase in the Reflected Intensity of X-Ray Films Using Photonic Crystals

    Science.gov (United States)

    Aly, Arafa H.; Eissa, M. F.

    Photographic film is the familiar image of recording X-ray method. Examinations performed with radiographic intensifying screens reduce the patient’s exposure to radiation of X-rays compared with those without radiographic intensifying screens, where it directs less than half of the light emitted from the X-ray film with a screen interaction. A reflective layer made of magnesium oxide or titanium dioxide is located between the screen and the base of the film; this layer can help regain the control of the header light in other directions and is forwarded to the film. One-dimensional array of photonic crystals (PCs) consists of MgO with Al and TiO2 with Al used as reflectors. This array may increase the reflected intensity by an amount of 10.88% if MgO-Al PCs with periodicity N=1 are used as reflectors.

  1. X-ray phase computed tomography for nanoparticulated imaging probes and therapeutics: preliminary feasibility study

    Science.gov (United States)

    Tang, Xiangyang; Yang, Yi; Tang, Shaojie

    2011-03-01

    With the scientific progress in cancer biology, pharmacology and biomedical engineering, the nano-biotechnology based imaging probes and therapeutical agents (namely probes/agents) - a form of theranostics - are among the strategic solutions bearing the hope for the cure of cancer. The key feature distinguishing the nanoparticulated probes/agents from their conventional counterparts is their targeting capability. A large surface-to-volume ratio in nanoparticulated probes/agents enables the accommodation of multiple targeting, imaging and therapeutic components to cope with the intra- and inter-tumor heterogeneity. Most nanoparticulated probes/agents are synthesized with low atomic number materials and thus their x-ray attenuation are very similar to biological tissues. However, their microscopic structures are very different, which may result in significant differences in their refractive properties. Recently, the investigation in the x-ray grating-based differential phase contrast (DPC) CT has demonstrated its advantages in differentiating low-atomic materials over the conventional attenuation-based CT. We believe that a synergy of x-ray grating-based DPC CT and nanoparticulated imaging probes and therapeutic agents may play a significant role in extensive preclinical and clinical applications, or even become a modality for molecular imaging. Hence, we propose to image the refractive property of nanoparticulated imaging probes and therapeutical agents using x-ray grating-based DPC CT. In this work, we conduct a preliminary feasibility study with a focus to characterize the contrast-to-noise ratio (CNR) and contrast-detail behavior of the x-ray grating-based DPC CT. The obtained data may be instructive to the architecture design and performance optimization of the x-ray grating-based DPC CT for imaging biomarker-targeted imaging probes and therapeutic agents, and even informative to the translation of preclinical research in theranostics into clinical applications.

  2. X-ray third-order nonlinear dynamical diffraction in a crystal

    Energy Technology Data Exchange (ETDEWEB)

    Balyan, M. K., E-mail: mbalyan@ysu.am [Yerevan State University, Faculty of Physics (Armenia)

    2015-12-15

    The dynamic diffraction of an X-ray wave in a crystal with a third-order nonlinear response to external field strength has been theoretically investigated. General equations for the wave propagation in crystal and nonlinear Takagi equations for both ideal and deformed crystals are derived. Integrals of motion are determined for the nonlinear problem of dynamic diffraction. The results of the numerical calculations of reflectivity in the symmetric Laue geometry for an incident plane wave and the intensity distributions on the output crystal surface for a point source are reported as an example.

  3. Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase.

    Science.gov (United States)

    Oksanen, E; Blakeley, M P; Bonneté, F; Dauvergne, M T; Dauvergne, F; Budayova-Spano, M

    2009-10-06

    Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05-1.20 A) and neutron diffraction data (1.9-2.5 A) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H(2)O and D(2)O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis.

  4. Nano-crystal growth in cordierite glass ceramics studied with X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Bras, Wim; Clark, Simon M.; Greaves, G. N.; Kunz, Martin; van Beek, W.; Radmilovic, V.

    2009-01-16

    The development of monodisperse crystalline particles in cordierite glass doped with Cr3+ after a two-step heat treatment is elucidated by a combination of time-resolved small and wide angle x-ray scattering (SAXS/WAXS) experiments with electron microscopy. The effects of bulk and surface crystallization can clearly be distinguished, and the crystallization kinetics of the bulk phase is characterized. The internal pressure due to structural differences between the crystalline and amorphous phase is measured but the physical cause of this pressure can not unambiguously be attributed. The combined measurements comprise a nearly full characterization of the crystallization processes and the resulting sample morphology.

  5. Dynamic crystal rotation resolved by high-speed synchrotron X-ray Laue diffraction.

    Science.gov (United States)

    Huang, J W; E, J C; Huang, J Y; Sun, T; Fezzaa, K; Luo, S N

    2016-05-01

    Dynamic compression experiments are performed on single-crystal Si under split Hopkinson pressure bar loading, together with simultaneous high-speed (250-350 ns resolution) synchrotron X-ray Laue diffraction and phase-contrast imaging. A methodology is presented which determines crystal rotation parameters, i.e. instantaneous rotation axes and angles, from two unindexed Laue diffraction spots. Two-dimensional translation is obtained from dynamic imaging by a single camera. High-speed motion of crystals, including translation and rotation, can be tracked in real time via simultaneous imaging and diffraction.

  6. Dynamic crystal rotation resolved by high-speed synchrotron X-ray Laue diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Huang, J. W.; E, J. C.; Huang, J. Y.; Sun, T.; Fezzaa, K.; Luo, S. N.

    2016-03-30

    Dynamic compression experiments are performed on single-crystal Si under split Hopkinson pressure bar loading, together with simultaneous high-speed (250–350 ns resolution) synchrotron X-ray Laue diffraction and phase-contrast imaging. A methodology is presented which determines crystal rotation parameters,i.e.instantaneous rotation axes and angles, from two unindexed Laue diffraction spots. Two-dimensional translation is obtained from dynamic imaging by a single camera. High-speed motion of crystals, including translation and rotation, can be tracked in real timeviasimultaneous imaging and diffraction.

  7. Cylindrical crystals of molybdenite-3R:sem- and x-ray investigations

    Science.gov (United States)

    Yushkin, N.; Zhabin, A.

    2003-04-01

    Flat faces are the characteristic feature of ionic crystals; nevertheless, among them there are cleavage-faced ones, up to the crystals with cylindrical shapes. More often they occur among minerals with layer structure or minerals with higher tendency to structural defectiveness (cylindrite, franckeite, asbestos, jamesonite, boulangerite and etc.). We studied exotic cylindrical crystals of molybdenite, discovered in the pegmatite veins of Slyudyanogorsky deposit of muscovite in Middle Ural by Kobyashev Yu. S., Zverev G. F. in 1973. Crystals have cylindrical shape, sometimes with sharpened or flattened wedge-shaped edges. Their length is 2-10 mm, diameter 0.8-mm. At the cross section crystals possess concentrically-laminar composition with tabulated axled canal with diameter about 120mkm. Thin layers arise packages about 15 mkm thickness. In the section crystals are fixed up to 6 such packages visually as well as by methods of X-ray phase-dispersed introscopy. According to the data of monocrystal and powder X-ray molybdenite represents as trigonal polytype 3R-R3m with insignificant quantity of hexagonal polytype 2H-P6@3/mmc. Twisting of leaf-like crystalline germs is one of the reasons of formation of cylindrical crystals due to syngenetic shistosity of containing rocks with crystallization.

  8. Evaluation of undoped ZnS single crystal materials for x-ray imaging applications

    Science.gov (United States)

    Saleh, Muad; Lynn, Kelvin G.; McCloy, John S.

    2017-05-01

    ZnS-based materials have a long history of use as x-ray luminescent materials. ZnS was one of the first discovered scintillators and is reported to have one of the highest scintillator efficiencies. The use of ZnS for high energy luminescence has been thus far limited to thin powder screens, such as ZnS:Ag which is used for detecting alpha radiation, due to opacity to its scintillation light, primarily due to scattering. ZnS in bulk form (chemical vapor deposited, powder processed, and single crystal) has high transmission and low scattering compared to powder screens. In this paper, the performance of single crystalline ZnS is evaluated for low energy x-ray (PLE) of several undoped ZnS single crystals is compared to their Radioluminescence (RL) spectra. It was found that the ZnS emission wavelength varies on the excitation source energy.

  9. X-Ray Reflectivity from the Surface of a Liquid Crystal:

    DEFF Research Database (Denmark)

    Pershan, P.S.; Als-Nielsen, Jens Aage

    1984-01-01

    X-ray reflectivity from the surface of a nematic liquid crystal is interpreted as the coherent superposition of Fresnel reflection from the surface and Bragg reflection from smectic order induced by the surface. Angular dependence of the Fresnel effect yields information on surface structure. Mea....... Measurement of the intensity of diffuse critical scattering relative to the Fresnel reflection yields the absolute value of the critical part of the density-density correlation function.......X-ray reflectivity from the surface of a nematic liquid crystal is interpreted as the coherent superposition of Fresnel reflection from the surface and Bragg reflection from smectic order induced by the surface. Angular dependence of the Fresnel effect yields information on surface structure...

  10. Instrument and method for X-ray diffraction, fluorescence, and crystal texture analysis without sample preparation

    Science.gov (United States)

    Gendreau, Keith (Inventor); Martins, Jose Vanderlei (Inventor); Arzoumanian, Zaven (Inventor)

    2010-01-01

    An X-ray diffraction and X-ray fluorescence instrument for analyzing samples having no sample preparation includes a X-ray source configured to output a collimated X-ray beam comprising a continuum spectrum of X-rays to a predetermined coordinate and a photon-counting X-ray imaging spectrometer disposed to receive X-rays output from an unprepared sample disposed at the predetermined coordinate upon exposure of the unprepared sample to the collimated X-ray beam. The X-ray source and the photon-counting X-ray imaging spectrometer are arranged in a reflection geometry relative to the predetermined coordinate.

  11. A secondary graphite crystal spectrometer for anomalous X-ray diffraction experiments

    CERN Document Server

    Stachs, O; Himmel, B; Gerber, T

    1999-01-01

    A new design for implementation of anomalous X-ray diffraction experiments is proposed. The exploitation of a graphite crystal spectrometer with good energy resolution in combination with an acceptable counting rate opens new possibilities to carry out AWAXS experiments and calculate partial structure functions. The proof of this measurement principle is demonstrated by presentation of the partial structure factor and radial distribution function for rubidium germanate glasses around the germanium component. (author)

  12. Calculations and surface quality measurements of high-asymmetry angle x-ray crystal monochromators for advanced x-ray imaging and metrological applications

    Science.gov (United States)

    Zápražný, Zdenko; Korytár, Dušan; Jergel, Matej; Šiffalovič, Peter; Dobročka, Edmund; Vagovič, Patrik; Ferrari, Claudio; Mikulík, Petr; Demydenko, Maksym; Mikloška, Marek

    2015-03-01

    We present the numerical optimization and the technological development progress of x-ray optics based on asymmetric germanium crystals. We show the results of several basic calculations of diffraction properties of germanium x-ray crystal monochromators and of an analyzer-based imaging method for various asymmetry factors using an x-ray energy range from 8 to 20 keV. The important parameter of highly asymmetric monochromators as image magnifiers or compressors is the crystal surface quality. We have applied several crystal surface finishing methods, including advanced nanomachining using single-point diamond turning (SPDT), conventional mechanical lapping, chemical polishing, and chemomechanical polishing, and we have evaluated these methods by means of atomic force microscopy, diffractometry, reciprocal space mapping, and others. Our goal is to exclude the chemical etching methods as the final processing technique because it causes surface undulations. The aim is to implement very precise deterministic methods with a control of surface roughness down to 0.1 nm. The smallest roughness (˜0.3 nm), best planarity, and absence of the subsurface damage were observed for the sample which was machined using an SPDT with a feed rate of 1 mm/min and was consequently polished using a fine polishing 15-min process with a solution containing SiO2 nanoparticles (20 nm).

  13. Crystal-field and covalency effects in uranates: an X-ray spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Butorin, Sergei M. [Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); Kvashnina, Kristina O. [European Synchrotron Radiation Facility, CS40220, Grenoble (France); Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Resource Ecology, Dresden (Germany); Smith, Anna L. [Department of Radiation Science and Technology, TU Delft (Netherlands); Popa, Karin [European Commission, Joint Research Centre, Institute for Transuranium Elements, Karlsruhe (Germany); Martin, Philippe M. [CEA Marcoule, CEA, DEN, DTEC/SECA/LCC, Bagnols-sur-Ceze (France)

    2016-07-04

    The electronic structure of U{sup V}- and U{sup VI}-containing uranates NaUO{sub 3} and Pb{sub 3}UO{sub 6} was studied by using an advanced technique, namely X-ray absorption spectroscopy (XAS) in high-energy-resolution fluorescence-detection (HERFD) mode. Due to a significant reduction in core-hole lifetime broadening, the crystal-field splittings of the 5f shell were probed directly in HERFD-XAS spectra collected at the U 3d edge, which is not possible by using conventional XAS. In addition, the charge-transfer satellites that result from U 5f-O 2p hybridization were clearly resolved. The crystal-field parameters, 5f occupancy, and degree of covalency of the chemical bonding in these uranates were estimated by using the Anderson impurity model by calculating the U 3d HERFD-XAS, conventional XAS, core-to-core (U 4f-3d transitions) resonant inelastic X-ray scattering (RIXS), and U 4f X-ray photoelectron spectra. The crystal field was found to be strong in these systems and the 5f occupancy was determined to be 1.32 and 0.84 electrons in the ground state for NaUO{sub 3} and Pb{sub 3}UO{sub 6}, respectively, which indicates a significant covalent character for these compounds. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. In vacuo X-ray data collection from graphene-wrapped protein crystals

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Crawshaw, Adam D. [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Trincao, Jose; Aller, Pierre; Alcock, Simon; Nistea, Ioana [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Salgado, Paula S. [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2015-09-26

    A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer. The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.

  15. SU-E-I-44: Some Preliminary Analysis of Angular Distribution of X-Ray Scattered On Soft Tissues

    Energy Technology Data Exchange (ETDEWEB)

    Ganezer, K; Krmar, M; Cvejic, Z; Rakic, S; Pajic, B [University of Novi Sad, Novi Sad Serbia (Serbia)

    2015-06-15

    Purpose: The angular distribution of x-radiation scattered at small angles (up to 16 degrees) from several different animal soft tissue (skin, fat, muscle, retina, etc) were measured using standard equipment devoted to study of crystal structure which provides excellent geometry conditions of measurements. showed measurable differences for different tissues. In the simplest possible case when measured samples do not differ in structure (different concentration solutions) it can be seen that intensity of scattered radiation is decreasing function of the concentration and the peak of the maximum of scattering distribution depends on the concentration as well. Methods: An x-ray scattering profile usually consists of sharp diffraction peak; however some properties of the spatial profiles of scattered radiation as intensity, the peak position, height, area, FWHM, the ratio of peak heights, etc. Results: The data contained measurable differences for different tissues. In the simplest possible case when measured samples do not differ in structure (different concentration solutions) it can be seen that intensity of scattered radiation is decreasing function of the concentration and the peak of the maximum of scattering distribution depends on the concentration as well. Measurements of different samples in the very preliminary phase showed that simple biological material used in study showed slightly different scattering pattern, especially at higher angles (around 10degrees). Intensity of radiation scattered from same tissue type is very dependent on water content and several more parameters. Conclusion: This preliminary study using animal soft tissues on the angular distributions of scattered x-rays suggests that angular distributions of X-rays scattered off of soft tissues might be useful in distinguishing healthy tissue from malignant soft tissue.

  16. X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Vitova, Tonya

    2008-02-15

    The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu{sup 1+} and Cu{sup 2+}) and Fe (Fe{sup 2+} and Fe{sup 3+}) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn{sup 2+} and Mn{sup 3+} in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu{sup 1+}) and sixfold (Cu{sup 2+}) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with {sup 3}He{sup 2+} ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

  17. X-ray reflectivity reveals ionic structure at liquid crystal-aqueous interfaces.

    Science.gov (United States)

    Hallett, James E; Hayward, Dominic W; Arnold, Thomas; Bartlett, Paul; Richardson, Robert M

    2017-08-23

    Here X-ray reflectivity has been used to determine the structure of liquid crystal monolayers for different cyanobiphenyl homologues supported on aqueous solutions of two different salt species. Sodium iodide induces homeotropic ordering for all of the monolayer forming liquid crystal homologues studied here, and forms a Stern layer of iodide ions at the liquid crystal cyano headgroup, similar to the case of lipids or surfactants supported on electrolyte solutions. The liquid crystal headgroups were also found to penetrate into the water surface when binding with iodide ions. Sodium bromide, however, does not form the same localisation of ions close to a liquid crystal monolayer, and instead appears to produce no noticeable change in the scattering length density of the liquid crystal monolayer compared to pure water. However, on further compression the X-ray reflectivity dramatically changes, revealing the emergence of the so-called "trilayer" structure for 5CB and 8CB. This transition occurs at a lower areal density for sodium bromide than for pure water, and unlike for the uncompressed film, a layer of bromide ions was found at the trilayer-water interface.

  18. Spatial Distribution of Trehalose Dihydrate Crystallization in Tablets by X-ray Diffractometry.

    Science.gov (United States)

    Thakral, Naveen K; Yamada, Hiroyuki; Stephenson, Gregory A; Suryanarayanan, Raj

    2015-10-05

    Crystallization of trehalose dihydrate (C12H22O11·2H2O) was induced by storing tablets of amorphous anhydrous trehalose (C12H22O11) at 65% RH (RT). Our goal was to evaluate the advantages and limitations of two approaches of profiling spatial distribution of drug crystallization in tablets. The extent of crystallization, as a function of depth, was determined in tablets stored for different time-periods. The first approach was glancing angle X-ray diffractometry, where the penetration depth of X-rays was modulated by the incident angle. Based on the mass attenuation coefficient of the matrix, the depth of X-ray penetration was calculated as a function of incident angle, which in turn enabled us to "calculate" the extent of crystallization to different depths. In the second approach, the tablets were split into halves and the split surfaces were analyzed directly. Starting from the tablet surface and moving toward the midplane, XRD patterns were collected in 36 "regions", in increments of 0.05 mm. The results obtained by the two approaches were, in general, in good agreement. Additionally, the results obtained were validated by determining the "average" crystallization in the entire tablet by using synchrotron radiation in the transmission mode. The glancing angle method could detect crystallization up to ∼650 μm and had a "surface bias". Being a nondestructive technique, this method will permit repeated analyses of the same tablet at different time points, for example, during a stability study. However, split tablet analyses, while a "destructive" technique, provided comprehensive and unbiased depth profiling information.

  19. X-ray plane-wave diffraction effects in a crystal with third-order nonlinearity

    Energy Technology Data Exchange (ETDEWEB)

    Balyan, M. K., E-mail: mbalyan@ysu.am [Yerevan State University, Faculty of Physics (Armenia)

    2016-12-15

    The two-wave dynamical diffraction in the Laue geometry has been theoretically considered for a plane X-ray wave in a crystal with a third-order nonlinear response to the external field. An analytical solution to the problem stated is found for certain diffraction conditions. A nonlinear pendulum effect is analyzed. The nonlinear extinction length is found to depend on the incident-wave intensity. A pendulum effect of a new type is revealed: the intensities of the transmitted and diffracted waves periodically depend on the incidentwave intensity at a fixed crystal thickness. The rocking curves and Borrmann nonlinear effect are numerically calculated.

  20. Bent perfect crystals as X-ray focusing polychromators in symmetric Laue geometry.

    Science.gov (United States)

    Guigay, J P; Ferrero, C; Bhattacharyya, D; Mathon, O; Pascarelli, S

    2013-01-01

    The focusing properties of cylindrically bent crystals in symmetric Laue geometry are discussed using the formalism of Fresnel diffraction and the analytical solution of the Takagi-Taupin equations for a point source on the entrance surface. The existence of a focal shift in the dynamical focusing effect is pointed out and discussed. The present theoretical framework is applied to experiments performed at the energy-dispersive X-ray absorption spectroscopy beamline of the European Synchrotron Radiation Facility concerning the position and the size of the focal spot obtained from a polychromatic source at a large distance from the bent crystal.

  1. Interface structure in directly bonded silicon crystals studied by synchrotron X-ray diffraction

    DEFF Research Database (Denmark)

    Nielsen, Mourits; Feidenhans'l, R.; Howes, P.B.

    1999-01-01

    Fusion-bonded silicon wafers exhibit a superstructure at their common interface due to the spatial beating of the two crystal lattices. The superstructure consists of a network of screw dislocations with a period determined by the twist angle theta. By synchrotron X-ray diffraction, the periodic...... elastic modulation in the two crystals resulting from the dislocation network has been measured. The characteristic thickness of the modulated region is found to be inversely proportional to theta, reaching over 160 Angstrom for theta = 0.4 degrees. This behavior is reproduced in numerical simulations...

  2. Lightweight and High-Resolution Single Crystal Silicon Optics for X-ray Astronomy

    Science.gov (United States)

    Zhang, William W.; Biskach, Michael P.; Chan, Kai-Wing; Mazzarella, James R.; McClelland, Ryan S.; Riveros, Raul E.; Saha, Timo T.; Solly, Peter M.

    2016-01-01

    We describe an approach to building mirror assemblies for next generation X-ray telescopes. It incorporates knowledge and lessons learned from building existing telescopes, including Chandra, XMM-Newton, Suzaku, and NuSTAR, as well as from our direct experience of the last 15 years developing mirror technology for the Constellation-X and International X-ray Observatory mission concepts. This approach combines single crystal silicon and precision polishing, thus has the potential of achieving the highest possible angular resolution with the least possible mass. Moreover, it is simple, consisting of several technical elements that can be developed independently in parallel. Lastly, it is highly amenable to mass production, therefore enabling the making of telescopes of very large photon collecting areas.

  3. Preliminary studies of radiation coupling between remote soft X-ray laser amplifiers

    Energy Technology Data Exchange (ETDEWEB)

    Cairns, G. (Queen' s Univ., Belfast (United Kingdom). Dept. of Pure and Applied Physics); Lewis, C.L.S. (Queen' s Univ., Belfast (United Kingdom). Dept. of Pure and Applied Physics); MacPhee, A.G. (Queen' s Univ., Belfast (United Kingdom). Dept. of Pure and Applied Physics); Neely, D. (Queen' s Univ., Belfast (United Kingdom). Dept. of Pure and Applied Physics); Holden, M. (Essex Univ., Colchester (United Kingdom). Dept. of Physics); Krishnan, J. (Essex Univ., Colchester (United Kingdom). Dept. of Physics); Tallents, G.J. (Essex Univ., Colchester (United Kingdom). Dept. of Physics); Key, M.H. (Rutherford Appleton Lab., Chilton (United Kingdom). Central Laser Facility Oxford Univ. (United Kingdom). Clarendon Lab.); Norreys, P.N. (Rutherford Appleton Lab., Chilton (United Kingdom). Central Laser Facility); Smith, C.G. (Oxford Univ. (United Kingdom). Clarendon Lab.); Zhang, J. (Oxford Univ. (United Kingdom). Clarendon Lab.); Holden, P.B. (York Univ. (United Kingdom). Dept. of Comp

    1994-01-01

    Coupling of a soft X-ray laser beam with a relaying concave mirror in a sequentially pumped amplifier geometry using the Ne-like Ge system has been studied experimentally. Preliminary observations indicate an increase in the spatial coherence of the amplified relayed beam. In addition, near-field imaging of one of the amplifier plasmas shows a double-lobed intensity pattern of the emergent beam indicating refractive guiding of the amplified beam with components both normal and tangential to the target surface. (orig.)

  4. Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Edward B.; Gurda-Whitaker, Brittney; Govindasamy, Lakshmanan; McKenna, Robert [Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 (United States); Zolotukhin, Sergei [Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610 (United States); Muzyczka, Nicholas [Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610 (United States); Agbandje-McKenna, Mavis, E-mail: mckenna@ufl.edu [Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 (United States)

    2006-12-01

    Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. The diffraction data were subsequently processed and reduced with an overall R{sub sym} of 12.3% and a completeness of 89.0%. Based on the unit-cell volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 Å resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.

  5. Preliminary report for using X-rays as verification and authentication tool

    Energy Technology Data Exchange (ETDEWEB)

    Esch, Ernst Ingo [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Desimone, David J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lakis, Rollin Evan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-04-06

    We examined x-rays for the use as authentication and verification tool in treaty verification. Several x-ray pictures were taken to determine the quality and feasibility of x-rays for these tasks. This document describes the capability of the used x-ray system and outlines its parameters and possible use.

  6. Superoxide reductase from the syphilis spirochete Treponema pallidum: crystallization and structure determination using soft X-rays

    Energy Technology Data Exchange (ETDEWEB)

    Santos-Silva, Teresa; Trincão, José; Carvalho, Ana L.; Bonifácio, Cecília; Auchère, Françoise; Moura, Isabel; Moura, José J. G.; Romão, Maria J., E-mail: mromao@dq.fct.unl.pt [REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)

    2005-11-01

    Superoxide reductase is a non-haem iron-containing protein involved in resistance to oxidative stress. The oxidized form of the protein has been crystallized and its three-dimensional structure solved. A highly redundant X-ray diffraction data set was collected on a rotating-anode generator using Cu Kα X-ray radiation. Four Fe atoms were located in the asymmetric unit corresponding to four protein molecules arranged as a dimer of homodimers. Superoxide reductase is a 14 kDa metalloprotein containing a catalytic non-haem iron centre [Fe(His){sub 4}Cys]. It is involved in defence mechanisms against oxygen toxicity, scavenging superoxide radicals from the cell. The oxidized form of Treponema pallidum superoxide reductase was crystallized in the presence of polyethylene glycol and magnesium chloride. Two crystal forms were obtained depending on the oxidizing agents used after purification: crystals grown in the presence of K{sub 3}Fe(CN){sub 6} belonged to space group P2{sub 1} (unit-cell parameters a = 60.3, b = 59.9, c = 64.8 Å, β = 106.9°) and diffracted beyond 1.60 Å resolution, while crystals grown in the presence of Na{sub 2}IrCl{sub 6} belonged to space group C2 (a = 119.4, b = 60.1, c = 65.6 Å, β = 104.9°) and diffracted beyond 1.55 Å. A highly redundant X-ray diffraction data set from the C2 crystal form collected on a copper rotating-anode generator (λ = 1.542 Å) clearly defined the positions of the four Fe atoms present in the asymmetric unit by SAD methods. A MAD experiment at the iron absorption edge confirmed the positions of the previously determined iron sites and provided better phases for model building and refinement. Molecular replacement using the P2{sub 1} data set was successful using a preliminary trace as a search model. A similar arrangement of the four protein molecules could be observed.

  7. Diffraction and imaging study of imperfections of crystallized lysozyme with coherent X-rays

    Science.gov (United States)

    Hu, Z. W.; Chu, Y. S.; Lai, B.; Thomas, B. R.; Chernov, A. A.

    2004-01-01

    Phase-contrast X-ray diffraction imaging and high-angular-resolution diffraction combined with phase-contrast radiographic imaging were employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in the symmetric Laue case. The full-width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal was approximately 16.7 arcsec and imperfections including line defects, inclusions and other microdefects were observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the growth front and have been found to originate mostly in a central growth area and occasionally in outer growth regions. Inclusions of impurities or formations of foreign particles in the central growth region are resolved in the images with high sensitivity to defects. Slow dehydration led to the broadening of a fairly symmetric 4 4 0 rocking curve by a factor of approximately 2.6, which was primarily attributed to the dehydration-induced microscopic effects that are clearly shown in X-ray diffraction images. The details of the observed defects and the significant change in the revealed microstructures with drying provide insight into the nature of imperfections, nucleation and growth, and the properties of protein crystals.

  8. X-ray Imaging of MagLIF Experiments Using a Spherically-Bent Crystal Optic

    Science.gov (United States)

    Harding, E. C.; Gomez, M. R.; Jennings, C. A.; Knapp, P. F.; Slutz, S. A.; Sefkow, A. B.; Awe, T. J.; Hansen, S. B.; Peterson, K. J.; Hahn, K. D.; McBride, R. D.; Rochau, G. A.; Sinars, D. B.; Golovkin, I.

    2015-11-01

    The recent Magnetized Liner Inertial Fusion (MagLIF) experiments performed on Sandia's Z-machine produced significant thermonuclear DD fusion yields that were accompanied by observable x-ray emission [M.R. Gomez et. al., PRL (2014)]. The MagLIF experiments relied on a spherically-bent crystal optic to image portions of the x-ray continuum that were generated by the hot stagnation plasma. The images of stagnation show a long (6 to 8 mm) and narrow (~100 micron) column of x-ray emission with structure in both directions. This structure may be caused by variations in the electron temperature (Te) and density (ne) , as well as opacity variations in the surrounding Be pusher. Here we investigate the possible contributions from each of these effects. We will also discuss the development of a diagnostic technique in which Te and ne of the DD fuel are inferred from spectra emitted by Fe impurities that become ionized to a He-like charge state. Sandia National Labs is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DoE NNSA under contract DE-AC04-94AL85000.

  9. Single crystal X-ray structure of the artists' pigment zinc yellow

    Science.gov (United States)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold; Sanyova, Jana; Bendix, Jesper

    2017-08-01

    The artists' pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2- moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type.

  10. Effects of thermal expansion of the crystal lattice on x-ray crystal spectrometers used for fusion research

    Science.gov (United States)

    Delgado-Aparicio, L.; Bitter, M.; Podpaly, Y.; Rice, J.; Burke, W.; Sanchez del Rio, M.; Beiersdorfer, P.; Bell, R.; Feder, R.; Gao, C.; Hill, K.; Johnson, D.; Lee, S. G.; Marmar, E.; Pablant, N.; Reinke, M. L.; Scott, S.; Wilson, R.

    2013-12-01

    X-ray imaging crystal spectrometers with high spectral and spatial resolution are currently being used on magnetically confined fusion devices to infer the time history profiles of ion and electron temperatures as well as plasma flow velocities. The absolute measurement of flow velocities is important for optimizing various discharge scenarios and evaluating the radial electric field in tokamak and stellarator plasmas. Recent studies indicate that the crystal temperature must be kept constant to within a fraction of a degree to avoid changes of the interplanar 2d-spacing by thermal expansion that cause changes in the Bragg angle, which could be misinterpreted as Doppler shifts. For the instrumental parameters of the x-ray crystal spectrometer on Alcator C-Mod, where those thermal effects were investigated, a change of the crystal temperature by 1 °C causes a change of the lattice spacing of the order of Δd = 1 × 10-5 Å introducing a fictitious velocity drift of the order of ˜3 km s-1. This effect must be considered for x-ray imaging crystals spectrometers installed on LHD, KSTAR, EAST, J-TEXT, NSTX and, in the future, W7-X and ITER.

  11. A curved crystal spectrometer for energy calibration and spectral characterization of mammographic x-ray sources.

    Science.gov (United States)

    Hudson, L T; Deslattes, R D; Henins, A; Chantler, C T; Kessler, E G; Schweppe, J E

    1996-10-01

    Clinical efficacy of diagnostic radiology for mammographic examinations is critically dependent on source characteristics, detection efficiency, image resolution and applied high voltage. In this report we focus on means for evaluation of source-dependent issues including noninvasive determination of the applied high voltage, and characterization of intrinsic spectral distributions which in turn reflect the effects of added filtration and target and window contamination. It is shown that a particular form of x-ray curved crystal spectrometry with electronic imaging can serve to determine all relevant parameters within the confines of a standard clinical exposure.

  12. Determination of Ni(II) crystal structure by powder x-ray diffraction ...

    African Journals Online (AJOL)

    X-ray powder diffraction pattern was used to determine the length of the unit cell, “a”, the lattice structure type, and the number of atoms per unit cell of Ni(II) crystal. The “a” value was determined to be 23.66 ± 0.005 Å, particle size of 34.87 nm, volume 13.24 Å and Strain value ε = 9.8 x 10-3. The cell search on PXRD patterns ...

  13. X-ray fluorescence holography studies for a Cu{sub 3}Au crystal

    Energy Technology Data Exchange (ETDEWEB)

    Dąbrowski, K.M., E-mail: karol.dabrowski@uj.edu.pl; Dul, D.T.; Jaworska-Gołąb, T.; Rysz, J.; Korecki, P.

    2015-12-01

    In this work we show that performing a numerical correction for beam attenuation and indirect excitation allows one to fully restore element sensitivity in the three-dimensional reconstruction of the atomic structure. This is exemplified by a comparison of atomic images reconstructed from holograms measured for ordered and disordered phases of a Cu{sub 3}Au crystal that clearly show sensitivity to changes in occupancy of the atomic sites. Moreover, the numerical correction, which is based on quantitative methods of X-ray fluorescence spectroscopy, was extended to take into account the influence of a disturbed overlayer in the sample.

  14. High resolution x-ray and gamma ray imaging using diffraction lenses with mechanically bent crystals

    Science.gov (United States)

    Smither, Robert K [Hinsdale, IL

    2008-12-23

    A method for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation is provided. High quality mechanically bent diffracting crystals of 0.1 mm radial width are used for focusing the radiation and directing the radiation to an array of detectors which is used for analyzing their addition to collect data as to the location of the source of radiation. A computer is used for converting the data to an image. The invention also provides for the use of a multi-component high resolution detector array and for narrow source and detector apertures.

  15. Revisit of alpha-chitin crystal structure using high resolution X-ray diffraction data.

    Science.gov (United States)

    Sikorski, Pawel; Hori, Ritsuko; Wada, Masahisa

    2009-05-11

    High resolution synchrotron X-ray fiber diffraction data recorded from crab tendon chitin have been used to describe the crystal structure of alpha-chitin. Crystal structures at 100 and 300 K have been solved using restrained crystallographic refinement against diffraction intensities measured from the fiber diffraction patterns. The unit cell contains two polymer chains in a 2(1) helix conformation and in the antiparallel orientation. The best agreement between predicated and observed X-ray diffraction intensities is obtained for a model that includes two distinctive conformations of C6-O6 hydroxymethl group. Those conformations are different from what is proposed in the generally accepted alpha-chitin crystal structure (J. Mol. Biol. 1978, 120, 167-181). Based on refined positions of the O6 atoms, a network of hydrogen bonds involving O6 is proposed. This network of hydrogen bonds can explain the main features of the polarized FTIR spectra of alpha-chitin and sheds some light on the origin of splitting of the amide I band observed on alpha-chitin IR spectra.

  16. Redetermination of LaZn5 based on single crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Igor Oshchapovsky

    2012-01-01

    Full Text Available The crystal structure of the already known binary title compound LaZn5 (lanthanum pentazinc (space group P6/mmm, Pearson symbol hP6, CaCu5 structure type has been redetermined from single-crystal X-ray diffraction data. In contrast to previous determinations based on X-ray powder data [Nowotny (1942. Z. Metallkd. 34, 247–253; de Negri et al. (2008. Intermetallics, 16, 168–178], where unit-cell parameters and assignment of the structure type were reported, the present study reveals anisotropic displacement parameters for all atoms. The crystal structure consists of three crytallographically distinct atoms. The La atom (Wyckoff site 1a, site symmetry 6/mmm is surrounded by 18 Zn atoms and two La atoms. The coordination polyhedron around one of the Zn atoms (Wyckoff site 2c, site symmetry -6m2 is an icosahedron made up from three La and nine Zn atoms. The other Zn atom (Wyckoff site 3g, site symmetry mmm is surrounded by four La and eight Zn atoms. Bonding between atoms is explored by means of the TB–LMTO–ASA (tight-binding linear muffin-tin orbital atomic spheres approximation program package. The positive charge density is localized around La atoms, and the negative charge density is around Zn atoms, with weak covalent bonding between the latter.

  17. Nearest-neighbour distribution of distances in crystals from extended X-ray absorption fine structure

    Science.gov (United States)

    Fornasini, P.; Grisenti, R.; Dapiaggi, M.; Agostini, G.; Miyanaga, T.

    2017-07-01

    Extended X-ray absorption fine structure (EXAFS) is a powerful probe of the distribution of nearest-neighbour distances around selected atomic species. We consider here the effect of vibrational disorder in crystals. The potential of EXAFS for the accurate evaluation of the coefficient of bond thermal expansion and its temperature dependence is discussed, with the aim of stimulating and facilitating the comparison with the results from total scattering experiments. The meaning of the distribution asymmetry in crystals and its connection with the effective potential anharmonicity and the bond expansion is quantitatively explored by comparing the results for a number of different systems. The extent of the relative atomic vibrations perpendicular to the bond direction and the perpendicular to parallel anisotropy are correlated with the extent of lattice negative thermal expansion as well as with the ionic mobility in superionic crystals.

  18. Arabidopsis receptor-like cytoplasmic kinase BIK1: purification, crystallization and X-ray diffraction analysis.

    Science.gov (United States)

    Lal, Neeraj K; Fisher, Andrew J; Dinesh-Kumar, Savithramma P

    2016-10-01

    Receptor-like cytoplasmic kinases (RLCKs) in Arabidopsis play a central role in the integration of signaling input from various growth and immune signaling pathways. BOTRYTIS-INDUCED KINASE 1 (BIK1), belonging to the RLCK family, is an important player in defense against bacterial and fungal pathogens and in ethylene and brassinosteroid hormone signaling. In this study, the purification and crystallization of a first member of the class VI family of RLCK proteins, BIK1, are reported. BIK1 was crystallized using the microbatch-under-oil method. X-ray diffraction data were collected to 2.35 Å resolution. The crystals belonged to the monoclinic space group C2, with two monomers per asymmetric unit.

  19. A Preliminary X-ray Study of Murine Tnfaip8/Oxi-α

    Directory of Open Access Journals (Sweden)

    Daeun Lee

    2014-03-01

    Full Text Available Tnfaip8/oxidative stress regulated gene-α (Oxi-α is a novel protein expressed specifically in brain dopaminergic neurons and its over-expression has been reported to protect dopaminergic cells against OS-induced cell death. In this study, murine C165S mutant Tnfaip8/Oxi-α has been crystallized and X-ray data have been collected to 1.8 Å using synchrotron radiation. The crystal belonged to the primitive orthorhombic space group P21212, with unit-cell parameters a = 66.9, b = 72.3, c = 93.5 Å. A full structural determination is under way in order to provide insights into the structure-function relationships of this protein.

  20. Purification, crystallization and preliminary X-ray structural studies of a 7.2 kDa cytotoxin isolated from the venom of Daboia russelli russelli of the Viperidae family

    Science.gov (United States)

    Roy Choudhury, Subhasree; Gomes, Aparna; Gomes, Antony; Dattagupta, Jiban K.; Sen, Udayaditya

    2006-01-01

    A cytotoxin (MW 7.2 kDa) from Indian Russell’s viper (Daboia russelli russelli) venom possessing antiproliferative activity, cardiotoxicity, neurotoxicity and myotoxicity has been purified, characterized and crystallized. The crystals belong to the tetragonal space group P41, with unit-cell parameters a = b = 47.94, c = 50.2 Å. Larger crystals, which diffracted to 1.5 Å, were found to be twinned; diffraction data were therefore collected to 2.93 Å resolution using a smaller crystal. Molecular-replacement calculations identified two molecules of the protein in the asymmetric unit, which is in accordance with the calculated V M value. PMID:16511326

  1. Rotation of X-ray polarization in the glitches of a silicon crystal monochromator.

    Science.gov (United States)

    Sutter, John P; Boada, Roberto; Bowron, Daniel T; Stepanov, Sergey A; Díaz-Moreno, Sofía

    2016-08-01

    EXAFS studies on dilute samples are usually carried out by collecting the fluorescence yield using a large-area multi-element detector. This method is susceptible to the 'glitches' produced by all single-crystal monochromators. Glitches are sharp dips or spikes in the diffracted intensity at specific crystal orientations. If incorrectly compensated, they degrade the spectroscopic data. Normalization of the fluorescence signal by the incident flux alone is sometimes insufficient to compensate for the glitches. Measurements performed at the state-of-the-art wiggler beamline I20-scanning at Diamond Light Source have shown that the glitches alter the spatial distribution of the sample's quasi-elastic X-ray scattering. Because glitches result from additional Bragg reflections, multiple-beam dynamical diffraction theory is necessary to understand their effects. Here, the glitches of the Si(111) four-bounce monochromator of I20-scanning just above the Ni  K edge are associated with their Bragg reflections. A fitting procedure that treats coherent and Compton scattering is developed and applied to a sample of an extremely dilute (100 micromolal) aqueous solution of Ni(NO 3 ) 2 . The depolarization of the wiggler X-ray beam out of the electron orbit is modeled. The fits achieve good agreement with the sample's quasi-elastic scattering with just a few parameters. The X-ray polarization is rotated up to ±4.3° within the glitches, as predicted by dynamical diffraction. These results will help users normalize EXAFS data at glitches.

  2. Rotation of X-ray polarization in the glitches of a silicon crystal monochromator

    Energy Technology Data Exchange (ETDEWEB)

    Sutter, John P.; Boada, Roberto; Bowron, Daniel T.; Stepanov, Sergey A.; Díaz-Moreno, Sofía

    2016-07-06

    EXAFS studies on dilute samples are usually carried out by collecting the fluorescence yield using a large-area multi-element detector. This method is susceptible to the `glitches' produced by all single-crystal monochromators. Glitches are sharp dips or spikes in the diffracted intensity at specific crystal orientations. If incorrectly compensated, they degrade the spectroscopic data. Normalization of the fluorescence signal by the incident flux alone is sometimes insufficient to compensate for the glitches. Measurements performed at the state-of-the-art wiggler beamline I20-scanning at Diamond Light Source have shown that the glitches alter the spatial distribution of the sample's quasi-elastic X-ray scattering. Because glitches result from additional Bragg reflections, multiple-beam dynamical diffraction theory is necessary to understand their effects. Here, the glitches of the Si(111) four-bounce monochromator of I20-scanning just above the Ni Kedge are associated with their Bragg reflections. A fitting procedure that treats coherent and Compton scattering is developed and applied to a sample of an extremely dilute (100 micromolal) aqueous solution of Ni(NO3)2. The depolarization of the wiggler X-ray beam out of the electron orbit is modeled. The fits achieve good agreement with the sample's quasi-elastic scattering with just a few parameters. The X-ray polarization is rotated up to ±4.3° within the glitches, as predicted by dynamical diffraction. These results will help users normalize EXAFS data at glitches.

  3. Highly perfect thin films of SiC: X-ray double crystal diffractometry and X-ray double crystal topographic study

    Energy Technology Data Exchange (ETDEWEB)

    Chaudhuri, J.; Cheng, X. [Wichita State Univ., KS (United States). Dept. of Mechanical Engineering; Yuan, C. [Emcore Corp., Somerset, NJ 08873 (United States); Steckl, A.J. [Nanoelectronics Laboratory, Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, OH 45221-0030 (United States)

    1997-01-05

    The structure, strain and defect density of SiC thin films epitaxially deposited on 6H-SiC (0001), Si(111) and Si(001) from the single-source organosilane precursor silacyclobutane (c-C{sub 3}H{sub 6}SiH{sub 2}) were determined by X-ray double crystal diffractometry and topographic methods. All the films grown on Si were found to be 3C-SiC type. The films grown on 6H-SiC (0001) at 800 to 1000 C were found to be 3C-SiC type, whereas the films grown on 6H-SiC (0001) at 1100 C were a mixture of 3C, 4H and 6H polytypes of SiC. All the films grown on Si had very high defect densities. However, the defect density was reduced by a factor of 10{sup 4} for the films of similar thickness on 6H-SiC (0001), with the film grown at 900 C being the optimum one exhibiting structural properties nearly equal to those of the substrate. (orig.) 35 refs.

  4. A triple axis double crystal multiple reflection camera for ultra small angle X-ray scattering

    Science.gov (United States)

    Lambard, Jacques; Lesieur, Pierre; Zemb, Thomas

    1992-06-01

    To extend the domain of small angle X-ray scattering requires multiple reflection crystals to collimate the beam. A double crystal, triple axis X-ray camera using multiple reflection channel cut crystals is described. Procedures for measuring the desmeared scattering cross-section on absolute scale are described as well as the measurement from several typical samples : fibrils of collagen, 0.3 μm diameter silica spheres, 0.16 μm diameter interacting latex spheres, porous lignite coal, liquid crystals in a surfactant-water system, colloidal crystal of 0.32 μm diameter silica spheres. L'extension du domaine de diffusion des rayons-X vers les petits angles demande l'emploi de cristaux à réflexions multiples pour collimater le faisceau. Nous décrivons une caméra à rayons-X à trois axes où les réflexions multiples sont réalisées dans deux cristaux à gorge. Nous donnons ensuite les procédures de déconvolution pour obtenir la section efficace de diffusion en échelle absolue, ainsi que les résultats des mesures effectuées avec plusieurs échantillons typiques : fibres de collagène, sphères de silice de 0,3 μm de diamètre, sphères de latex de 0,16 μm de diamètre en interaction, charbon lignite poreux, cristaux liquides formés dans un système eau-tensioactif, solution colloïdale de sphères de silice de 0,32 μm de diamètre.

  5. Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

    Science.gov (United States)

    Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

    2014-12-11

    The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

  6. Crystallization and preliminary X-ray crystallographic analysis of the variable domain of Scl2.3, a streptococcal collagen-like protein from invasive M3-type Streptococcus pyogenes.

    Science.gov (United States)

    Squeglia, Flavia; Bachert, Beth; Romano, Maria; Lukomski, Slawomir; Berisio, Rita

    2013-09-01

    Streptococcal collagen-like proteins (Scls) are widely expressed by the well recognized human pathogen Streptococcus pyogenes. These surface proteins contain a signature central collagen-like region and an amino-terminal globular domain, termed the variable domain, which is protruded away from the cell surface by the collagen-like domain. Despite their recognized importance in bacterial pathogenicity, no structural information is presently available on proteins of the Scl class. The variable domain of Scl2 from invasive M3-type S. pyogenes has successfully been crystallized using vapour-diffusion methods. The crystals diffracted to 1.5 Å resolution and belonged to space group H32, with unit-cell parameters a = 44.23, b = 44.23, c = 227.83 Å. The crystal structure was solved by single-wavelength anomalous dispersion using anomalous signal from a europium chloride derivative.|

  7. Time-Resolved Soft X-ray Diffraction Reveals Transient Structural Distortions of Ternary Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Klaus Mann

    2009-11-01

    Full Text Available Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2–5.2 nm. The investigated system was the lyotropic liquid crystal C16E7/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 μs. Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 Å resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

  8. X-ray beam monitor made by thin-film CVD single-crystal diamond.

    Science.gov (United States)

    Marinelli, Marco; Milani, E; Prestopino, G; Verona, C; Verona-Rinati, G; Angelone, M; Pillon, M; Kachkanov, V; Tartoni, N; Benetti, M; Cannatà, D; Di Pietrantonio, F

    2012-11-01

    A novel beam position monitor, operated at zero bias voltage, based on high-quality chemical-vapor-deposition single-crystal Schottky diamond for use under intense synchrotron X-ray beams was fabricated and tested. The total thickness of the diamond thin-film beam monitor is about 60 µm. The diamond beam monitor was inserted in the B16 beamline of the Diamond Light Source synchrotron in Harwell (UK). The device was characterized under monochromatic high-flux X-ray beams from 6 to 20 keV and a micro-focused 10 keV beam with a spot size of approximately 2 µm × 3 µm square. Time response, linearity and position sensitivity were investigated. Device response uniformity was measured by a raster scan of the diamond surface with the micro-focused beam. Transmissivity and spectral responsivity versus beam energy were also measured, showing excellent performance of the new thin-film single-crystal diamond beam monitor.

  9. Advanced spectroscopic investigation of color centers in LiF crystals exposed to 6 MV X-ray clinical beams

    Science.gov (United States)

    Vincenti, M. A.

    2017-03-01

    Polished LiF crystals were irradiated by using 6MV X-rays produced by a clinical linear accelerator. The irradiation doses (absorbed dose to water) covered the 1-100Gy range. Optical absorption spectra show stable formation of primary F defects, while the M absorption band, located at around 450nm and due to the aggregate F 2 and F 3+ color centers, was not detectable. By using the Smakula formula, a concentration of 1.2×10^{16} and 1.9×10^{16} F/cm ^{-3} was obtained for LiF crystals irradiated at 50 and 100Gy, respectively. Under argon laser excitation at 457.9nm, photoluminescence spectra of the irradiated LiF crystals exhibited the characteristic F 2 and F 3+ broad emission bands. The integrated photoluminescence intensity of F 2 and F 3+ defects as a function of the irradiation dose shows a linear behaviour in the investigated dose range. This result is confirmed by the measurements of the F 2 and F 3+ integrated photoluminescence intensity performed by using a conventional fluorescence optical microscope under blue lamp illumination. These preliminary experimental results are encouraging for further investigation of nominally pure LiF crystals as clinical dosimeters based on optical reading of photoluminescence emitted by radiation-induced color centers.

  10. Crystallization and X-ray diffraction analysis of human CLEC-2

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Aleksandra A.; O’Callaghan, Christopher A., E-mail: chrisoc@ccmp.ox.ac.uk [Henry Wellcome Building of Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2005-12-01

    Recombinant human CLEC-2 was crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and X-ray diffraction data were collected to 2.0 Å. The human C-type lectin-like protein CLEC-2 has recently been shown to be expressed on the surface of platelets and to function as a receptor for the snake-venom protein rhodocytin. The C-type lectin-like domain (CTLD) of CLEC-2 was expressed in Escherichia coli, refolded and purified. Crystals of this recombinant CLEC-2 were grown by sitting-drop vapour diffusion using polyethylene glycol (PEG) 6000 as a precipitant. After optimization, crystals were grown which diffracted to 2.0 Å using in-house radiation (λ = 1.5418 Å). These crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 35.407, b = 55.143, c = 56.078 Å. The presence of one molecule per asymmetric unit is consistent with a crystal volume per unit weight (V{sub M}) of 1.82 Å{sup 3} Da{sup −1} and a solvent content of 32.6%. These results suggest that crystals producing diffraction of this quality will be suitable for the structural determination of human CLEC-2.

  11. Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Kovalevsky, A.Y.; Fisher, S.Z.; Seaver, S.; Mustyakimov, M.; Sukumar, N.; Langan, P.; Mueser, T.C.; Hanson, B.L. (Toledo); (Cornell); (LANL)

    2010-08-18

    Room-temperature and 100 K X-ray and room-temperature neutron diffraction data have been measured from equine cyanomethemoglobin to 1.7 {angstrom} resolution using a home source, to 1.6 {angstrom} resolution on NE-CAT at the Advanced Photon Source and to 2.0 {angstrom} resolution on the PCS at Los Alamos Neutron Science Center, respectively. The cyanomethemoglobin is in the R state and preliminary room-temperature electron and neutron scattering density maps clearly show the protonation states of potential Bohr groups. Interestingly, a water molecule that is in the vicinity of the heme group and coordinated to the distal histidine appears to be expelled from this site in the low-temperature structure.

  12. Crystallization and preliminary X-ray diffraction analysis of the P3 RNA domain of yeast ribonuclease MRP in a complex with RNase P/MRP protein components Pop6 and Pop7.

    Science.gov (United States)

    Perederina, Anna; Esakova, Olga; Quan, Chao; Khanova, Elena; Krasilnikov, Andrey S

    2010-01-01

    Eukaryotic ribonucleases P and MRP are closely related RNA-based enzymes which contain a catalytic RNA component and several protein subunits. The roles of the protein subunits in the structure and function of eukaryotic ribonucleases P and MRP are not clear. Crystals of a complex that included a circularly permuted 46-nucleotide-long P3 domain of the RNA component of Saccharomyces cerevisiae ribonuclease MRP and selenomethionine derivatives of the shared ribonuclease P/MRP protein components Pop6 (18.2 kDa) and Pop7 (15.8 kDa) were obtained using the sitting-drop vapour-diffusion method. The crystals belonged to space group P4(2)22 (unit-cell parameters a = b = 127.2, c = 76.8 A, alpha = beta = gamma = 90 degrees ) and diffracted to 3.25 A resolution.

  13. Purification, crystallization and preliminary X-ray data collection of the N-terminal domain of the 26S proteasome regulatory subunit p27 and its complex with the ATPase domain of Rpt5 from Mus musculus.

    Science.gov (United States)

    Diao, Wentao; Yang, Xue; Zhou, Hao

    2014-05-01

    The protein 26S proteasome regulatory subunit p27 is one of the four chaperones that help in the assembly of the 19S regulatory particle (RP) of the 26S proteasome. In the present work, the N-terminus of p27 (residues 1-128) from Mus musculus was cloned, expressed, purified and crystallized alone and in complex with the C-terminal ATPase domain of Rpt5 (residues 173-442). The crystals of p27((1-128)) diffracted to 1.7 Å resolution and belonged to space group P212121, with unit-cell parameters a = 26.79, b = 30.39, c = 145.06 Å. Resolution-dependent Matthews coefficient probability analysis suggested the presence of only one molecule per asymmetric unit, with 40.5% solvent content and a VM value of 2.02 Å(3) Da(-1). The crystal of the p27((1-128))-Rpt5((173-442)) complex diffracted to 4 Å resolution and belonged to space group P222, with unit-cell parameters a = 75.93, b = 76.08, c = 336.85 Å. The presence of four heterodimers in the asymmetric unit with 53.2% solvent content and a VM value of 2.63 Å(3) Da(-1) or five heterodimers in the asymmetric unit with 41.5% solvent content and a VM value of 2.10 Å(3) Da(-1) is assumed.

  14. Crystallization and preliminary X-ray analysis of the splice variant of human ankyrin repeat and suppressor of cytokine signaling box protein 9 (hASB9-2).

    Science.gov (United States)

    Fei, Xiangwei; Zhang, Yong; Gu, Xing; Qiu, Rui; Mao, Yumin; Ji, Chaoneng

    2008-01-01

    Human ankyrin repeat and suppressor of cytokine signaling box protein 9 (hASB9), a subunit of an Elongin C-cullin-SOCS box (ECS) E3 ubiquitin ligase complex, is believed to be involved in specific substrate-recognition for ubiquitination and degradation. In fact, this specific substrate-recognition is determined by the ankyrin repeats of hASB9 protein. Here, we have cloned and overexpressed the hASB9-2, the splice variant of hASB9 with only one ankyrin repeat domain, as a 6His-tagged recombinant protein in Escherichia coli. The purified hASB9-2 protein was crystallized by the hanging-drop vapor-diffusion technique and diffracted to 2.2A resolution. The data showed that the cubic hASB9-2 crystal belongs to space group P4(3)32 with unit-cell parameters (a=b=c=129.25A, alpha=beta=gamma=90 degrees ). An asymmetric unit in the crystal was assumed to contain one protein molecule giving the Matthews Coefficient factor of 2.81 and the solvent content of 56.3%.

  15. X-ray-excited optical luminescence of protein crystals: a new tool for studying radiation damage during diffraction data collection.

    Science.gov (United States)

    Owen, Robin L; Yorke, Briony A; Pearson, Arwen R

    2012-05-01

    During X-ray irradiation protein crystals radiate energy in the form of small amounts of visible light. This is known as X-ray-excited optical luminescence (XEOL). The XEOL of several proteins and their constituent amino acids has been characterized using the microspectrophotometers at the Swiss Light Source and Diamond Light Source. XEOL arises primarily from aromatic amino acids, but the effects of local environment and quenching within a crystal mean that the XEOL spectrum of a crystal is not the simple sum of the spectra of its constituent parts. Upon repeated exposure to X-rays XEOL spectra decay non-uniformly, suggesting that XEOL is sensitive to site-specific radiation damage. However, rates of XEOL decay were found not to correlate to decays in diffracting power, making XEOL of limited use as a metric for radiation damage to protein crystals. © 2012 International Union of Crystallography

  16. High-resolution x-ray characterization of mosaic crystals for hard x-and gamma-ray astronomy

    Science.gov (United States)

    Ferrari, Claudio; Buffagni, Elisa; Marchini, Laura; Zappettini, Andrea

    2011-09-01

    We have analyzed GaAs, Cu, CdTe, and CdZnTe crystals as possible optical elements for hard x-ray lenses for x-ray astronomy. We used high resolution x-ray diffraction at 8keV in Bragg geometry and Laue transmission diffraction at synchrotron at energies up to 500 keV. A good agreement was found between the mosaicity evaluated in Bragg diffraction geometry with x-ray penetration of the order of few tens micrometers and in Laue transmission geometry at synchrotron. All the analyzed crystals showed mosaicity values in a range between a few to 150 arcseconds and suitable for the application. Nevertheless -CdTe and CdZnTe crystals exhibit non-uniformity due to the presence of low angle grain boundaries; -Cu crystals exhibit mosaicity of the order of several arcminutes; they indeed suffer by a severe cutting damage that had to be removed with a very deep etching. The FWHM was also rapidly decreasing with the x-ray energy showing that the mosaic spread is not the only origin of peak broadening; -GaAs crystals grown by Czochralski method show mosaicity up to 30 arcseconds and good diffraction efficiency up to energies of 500 keV. The use of thermal treatments as a possible method to increase the mosaic spread is also evaluated.

  17. Crystallization and preliminary X-ray analysis of the type IV restriction endonuclease ScoMcrA from Streptomyces coelicolor, which cleaves both Dcm-methylated DNA and phosphorothioated DNA.

    Science.gov (United States)

    Liu, Guang; Zhang, Zhenyi; Zhao, Gong; Deng, Zixin; Wu, Geng; He, Xinyi

    2015-01-01

    ScoMcrA is a type IV modification-dependent restriction endonuclease found in the model strain Streptomyces coelicolor. Unlike type I, II and III restriction endonucleases, which cleave unmodified DNA, type IV restriction endonucleases cleave modified DNA, including methylated, hydroxymethylated, glucosyl-hydroxymethylated and phosphorothioated DNA. ScoMcrA targets both Dcm-methylated DNA and phosphorothioated DNA, and makes double-strand breaks 16-28 nt away from the modified nucleotides or the phosphorothioate links. However, the mechanism by which ScoMcrA recognizes these two entirely different types of modification remains unclear. In this study, the ScoMcrA protein was overexpressed, purified and crystallized. The crystals diffracted to 3.35 Å resolution and belonged to space group P2(1)2(1)2(1). The unit-cell parameters were determined to be a=130.19, b=139.36, c=281.01 Å, α=β=γ=90°. These results will facilitate the detailed structural analysis of ScoMcrA and further elucidation of its biochemical mechanism.

  18. Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P.

    Science.gov (United States)

    Sumida, Tomomi; Yanagisawa, Tatsuo; Ishii, Ryohei; Yokoyama, Shigeyuki

    2010-09-01

    GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, was overexpressed in E. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (LysAMS) by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The GenX-LysAMS crystals belonged to the triclinic space group P1, with unit-cell parameters a=54.80, b=69.15, c=94.08 A, alpha=95.47, beta=106.51, gamma=90.46 degrees, and diffracted to 1.9 A resolution. Furthermore, GenX was cocrystallized with translation elongation factor P (EF-P), which is believed to be a putative substrate of GenX, and LysAMS using PEG 4000 and ammonium sulfate as precipitants. The GenX-EF-P-LysAMS crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a=105.93, b=102.96, c=119.94 A, beta=99.4 degrees, and diffracted to 2.5 A resolution. Structure determination of the E. coli GenX-LysAMS and GenX-EF-P-LysAMS complexes by molecular replacement was successful and structure refinements are now in progress.

  19. Preparation of bent crystals as high-efficiency optical elements for hard x-ray astronomy

    Science.gov (United States)

    Buffagni, Elisa; Ferrari, Claudio; Rossi, Francesca; Marchini, Laura; Zappettini, Andrea

    2012-05-01

    Curved crystals, instead of flat mosaic crystals, can be used as optical elements of a Laue lens for hard x- and gamma-ray astronomy to increase the diffraction efficiency. We propose to achieve the bending of the crystals by a controlled surface damaging, which introduces defects in a layer of few tens nanometers in thickness undergoing a highly compressive strain. Several oriented silicon and gallium arsenide wafer crystals have been treated. The local and mean curvature radii of each sample have been determined by means of high resolution x-ray diffraction measurements in Bragg condition at low energy (8 keV). Silicon samples showed spherical curvatures, whereas GaAs-treated samples evidenced elliptical curvatures with major axes corresponding to the crystallographic directions. Curvature radii between 3 and 70 m were easily obtained in wafers of different thicknesses. The characterization of GaAs samples performed in Laue geometry at gamma-ray energy of 120 keV confirmed the increase of the diffraction efficiency in the bent crystals.

  20. Crystallization and X-ray analysis of the salmon-egg lectin SEL24K

    Energy Technology Data Exchange (ETDEWEB)

    Murata, Kenji [Department of Animal Science, University of California, Davis 95616 (United States); Fisher, Andrew J. [Department of Chemistry, University of California, Davis 95616 (United States); Hedrick, Jerry L., E-mail: jlhedrick@ucdavis.edu [Department of Animal Science, University of California, Davis 95616 (United States)

    2007-05-01

    The 24 kDa egg lectin of Chinook salmon (Oncorhynchus tshawytscha) was purified by affinity chromatography from salmon eggs and crystallized by the hanging-drop vapor-diffusion method using 15/4 EO/OH (pentaerythritol ethoxylate) as a precipitant. The 24 kDa egg lectin of Chinook salmon (Oncorhynchus tshawytscha) is released from the egg during the cortical reaction. The lectin functions in blocking polyspermy during the fertilization process. The egg lectin was purified by affinity chromatography from salmon eggs and crystallized by the hanging-drop vapor-diffusion method using 15/4 EO/OH (pentaerythritol ethoxylate) as a precipitant. The crystal diffracted synchrotron-radiation X-rays to 1.63 Å resolution. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 93.0, b = 73.6, c = 113.6 Å, α = 90, β = 92.82, γ = 90°. The crystal is likely to contain eight molecules in the asymmetric unit (V{sub M} = 2.3 Å{sup 3} Da{sup −1}), corresponding to a solvent content of 45.5%. A self-rotation function suggests an arrangement with 222 point symmetry within the asymmetric unit.

  1. Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

    DEFF Research Database (Denmark)

    Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith

    2016-01-01

    The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... is not a packing effect, but caused by intramolecular steric hindrance....

  2. X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.

    Science.gov (United States)

    Catalano, Alessia; Luciani, Rosaria; Carocci, Alessia; Cortesi, Debora; Pozzi, Cecilia; Borsari, Chiara; Ferrari, Stefania; Mangani, Stefano

    2016-11-10

    Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that species-specific inhibition of the protein can be achieved despite the relatively high structural similarity among bacterial TSs and human TS. We had previously obtained the EfTS crystal structure of the protein in complex with the metabolite 5-formyl-tetrahydrofolate (5-FTHF) suggesting the protein role as metabolite reservoir; however, protein-inhibitors complexes were still missing. In the present work we identified some inhibitors bearing the phthalimidic core from our in-house library and we performed crystallographic screening towards EfTS. We obtained two X-ray crystallographic structures: the first with a weak phthalimidic inhibitor bound in one subunit and 5-hydroxymethylene-6-hydrofolic acid (5-HMHF) in the other subunit; a second X-ray structure complex with methotrexate. The structural information achieved confirm the role of EfTS as an enzyme involved in the folate pool system and provide a structural basis for structure-based drug design. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  3. On the possibility of using X-ray Compton scattering to study magnetoelectrical properties of crystals

    Energy Technology Data Exchange (ETDEWEB)

    Collins, S. P., E-mail: steve.collins@diamond.ac.uk; Laundy, D.; Connolley, T.; Laan, G. van der; Fabrizi, F. [Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE (United Kingdom); Janssen, O. [Department of Physics, New York University, New York, NY 10003 (United States); Cooper, M. J. [Department of Physics, University of Warwick, CV4 7AL (United Kingdom); Ebert, H.; Mankovsky, S. [Universität München, Department Chemie, Haus E2.033, Butenandtstrasse 5-13, D-81377 München (Germany)

    2016-02-16

    The possibility of using X-ray Compton scattering to reveal antisymmetric components of the electron momentum density, as a fingerprint of magnetoelectric sample properties, is investigated experimentally and theoretically by studying the polar ferromagnet GaFeO{sub 3}. This paper discusses the possibility of using Compton scattering – an inelastic X-ray scattering process that yields a projection of the electron momentum density – to probe magnetoelectrical properties. It is shown that an antisymmetric component of the momentum density is a unique fingerprint of such time- and parity-odd physics. It is argued that polar ferromagnets are ideal candidates to demonstrate this phenomenon and the first experimental results are shown, on a single-domain crystal of GaFeO{sub 3}. The measured antisymmetric Compton profile is very small (≃ 10{sup −5} of the symmetric part) and of the same order of magnitude as the statistical errors. Relativistic first-principles simulations of the antisymmetric Compton profile are presented and it is shown that, while the effect is indeed predicted by theory, and scales with the size of the valence spin–orbit interaction, its magnitude is significantly overestimated. The paper outlines some important constraints on the properties of the antisymmetric Compton profile arising from the underlying crystallographic symmetry of the sample.

  4. X-Ray Damage to the Mn4Ca Complex in Single Crystals of Photosystem II: A Case Study for Metalloprotein Crystallography

    National Research Council Canada - National Science Library

    Junko Yano; Jan Kern; Klaus-Dieter Irrgang; Matthew J. Latimer; Uwe Bergmann; Pieter Glatzel; Yulia Pushkar; Jacek Biesiadka; Bernhard Loll; Kenneth Sauer; Johannes Messinger; Athina Zouni; Vittal K. Yachandra; Judith P. Klinman

    2005-01-01

    X-ray absorption spectroscopy was used to measure the damage caused by exposure to x-rays to the Mn Ca active site in single crystals of photosystem II as a function of dose and energy of x-rays, temperature, and time...

  5. Preliminary X-ray crystallographic studies of yeast mitochondrial protein Tom70p

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yunkun [Department of Cell Biology, Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham (United States); McCombs, Debbie; Nagy, Lisa; DeLucas, Lawrence [Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham (United States); Sha, Bingdong, E-mail: bdsha@uab.edu [Department of Cell Biology, Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham (United States)

    2006-03-01

    Tom70p is an important translocase of the outer membrane complex member and a major surface receptor of the protein-translocation machinery in the outer mitochondrial membrane. To investigate the mechanism by which Tom70p functions to deliver the mitochondrial protein precursors, the cytosolic fragment of yeast Tom70p (cTom70p) has been crystallized. Protein translocations across mitochondrial membranes play critical roles in mitochondrion biogenesis. Protein transport from the cell cytosol to the mitochondrial matrix is carried out by the translocase of the outer membrane (TOM) complex and the translocase of the inner membrane (TIM) complexes. Tom70p is an important TOM-complex member and a major surface receptor of the protein-translocation machinery in the outer mitochondrial membrane. To investigate the mechanism by which Tom70p functions to deliver the mitochondrial protein precursors, the cytosolic fragment of yeast Tom70p (cTom70p) was crystallized. The crystals diffract to 3.2 Å using a synchrotron X-ray source and belong to space group P2{sub 1}, with unit-cell parameters a = 44.89, b = 168.78, c = 83.41 Å, α = 90.00, β = 102.74, γ = 90.00°. There are two Tom70p molecules in one asymmetric unit, which corresponds to a solvent content of approximately 51%. Structure determination by MAD methods is under way.

  6. Analysis and implementation of a space resolving spherical crystal spectrometer for x-ray Thomson scattering experiments.

    Science.gov (United States)

    Harding, E C; Ao, T; Bailey, J E; Loisel, G; Sinars, D B; Geissel, M; Rochau, G A; Smith, I C

    2015-04-01

    The application of a space-resolving spectrometer to X-ray Thomson Scattering (XRTS) experiments has the potential to advance the study of warm dense matter. This has motivated the design of a spherical crystal spectrometer, which is a doubly focusing geometry with an overall high sensitivity and the capability of providing high-resolution, space-resolved spectra. A detailed analysis of the image fluence and crystal throughput in this geometry is carried out and analytical estimates of these quantities are presented. This analysis informed the design of a new spectrometer intended for future XRTS experiments on the Z-machine. The new spectrometer collects 6 keV x-rays with a spherically bent Ge (422) crystal and focuses the collected x-rays onto the Rowland circle. The spectrometer was built and then tested with a foam target. The resulting high-quality spectra prove that a spherical spectrometer is a viable diagnostic for XRTS experiments.

  7. Optical and X-ray absorption spectroscopy in lead doped lithium fluoride crystals

    Energy Technology Data Exchange (ETDEWEB)

    Somma, F; Aloe, P; D' Acapito, F; Montereali, R M; Polosan, S; Secu, M; Vincenti, M A, E-mail: somma@fis.uniroma3.it

    2010-11-15

    LiF:Pb doped crystals were successfully grown by Kyropoulos method, starting with drying powders. The presence of Pb{sup 2+} ions in the LiF crystals were evidenced by the absorption band at 278 nm and by 375 nm photoluminescence. The presence of some other Pb structures with oxygen compounds in the as made samples was evidenced, decreasing after some annealing procedures. The local environment and valence state of Pb in LiF were studied by X-ray Absorption Spectroscopy at the Pb L{sub III} and L{sub I} edges. XANES data reveal that Pb is present as Pb{sup 2+} whereas EXAFS data show that it is incorporated in the crystal and not forming PbF{sub 2} precipitates. Identical spectra are obtained for samples as prepared and after thermal annealing up to 650 deg. C demonstrating the stability of the incorporation site. Also the concentration of Pb in the crystal has no effect on the location site of the metal as the same spectrum is obtained for specimens with different dopant concentrations.

  8. X-Ray diffraction study of KTiOPO{sub 4} single crystals doped with hafnium

    Energy Technology Data Exchange (ETDEWEB)

    Novikova, N. E., E-mail: natnov@ns.crys.ras.ru; Verin, I. A.; Sorokina, N. I.; Alekseeva, O. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Orlova, E. I.; Voronkova, V. I. [Moscow State University, Faculty of Physics (Russian Federation)

    2011-05-15

    Single crystals of KTi{sub 1-x}Hf{sub x}OPO{sub 4} (x = 0.015(2), 0.035(1), and 0.128(1) are reinvestigated by precision X-ray diffraction at room temperature. It is found that the implantation of hafnium atoms in the crystal structure of KTiOPO{sub 4} does not lead to significant changes in the framework and affects only the positions of the potassium atoms in the channel. Our studies reveal the displacements of the potassium atoms from their main and additional positions in the structure of pure KTP in all three structures studied. The largest displacements from the K1 Prime and K1 Double-Prime additional positions are observed in the structure with x = 0.035. At this hafnium concentration, the occupancy of the main positions of potassium atoms decreases and the occupancy of the additional positions increases in relation to those in KTP. This redistribution of potassium atoms enhances the nonuniformity of distribution of the electron density in the vicinity of their positions, which is probably responsible for the increase in the nonlinear susceptibility of KTP crystals that contain 3.5% hafnium in relation to crystals of pure KTP.

  9. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N., E-mail: nahum@ufpa.b [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Ciencias Exatas e Naturais; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica

    2010-07-01

    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  10. Heteroaryl Chalcones: Design, Synthesis, X-ray Crystal Structures and Biological Evaluation

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2013-10-01

    Full Text Available Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a–i containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and reducing power abilities. The results indicate the tested compounds show a varied range of inhibition values against all the tested microbial strains. Compound 3c with a p-fluoro substituent on the phenyl ring exhibits elevated antimicrobial activity, whereas the compounds 3e and 3f displayed the least antimicrobial activities. The compounds 3d, 3e, 3f and 3i showed good ferric and cupric reducing abilities, and the compounds 3b and 3c showed the weakest reducing power in the series.

  11. Triple crystal x-ray diffraction analysis of chemical-mechanical polished gallium arsenide

    Science.gov (United States)

    Wang, V. S.; Matyi, R. J.

    1992-12-01

    High-resolution triple crystal x-ray diffraction has been used to monitor the magnitude of diffuse scattering from chemical-mechanical (CM) polished GaAs. The diffuse scattering, which is attributed to kinematic scattering arising from polish-induced crystallographic defects, was found to be only slightly affected when each of four CM polish parameters (bromine concentration in Br2/methanol, total polish time, polish pad rotation speed, and force on sample) was varied individually. The combined effect of increases in both the pad rotation speed and the force on the sample increased the magnitude of the diffuse scattering, suggesting the generation of mechanical damage. When all four variables were increased to their maximum values, the diffuse scattering increased dramatically and became anisotropic. We have expressed the magnitude of the diffuse scattering in terms of an ``excess intensity'' in reciprocal space to provide a semi-quantitative relation between CM polish parameters and the generation of polish-induced damage.

  12. Life in the fast lane for protein crystallization and X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D. (UAH); (NASA); (Georgia)

    2010-07-20

    The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain 'low-hanging fruit' protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area

  13. Preliminary design and R&D of ITER diagnostic-radial X-ray camera

    Science.gov (United States)

    Hu, L.; Chen, K.; Chen, Y.; Cao, H.; Li, S.; Yu, H.; Zhan, J.; Shen, J.; Qin, S.; Sheng, X.; Zhao, J.; Niu, L.; Feng, C.; Ge, J.; Zhang, S.; Zhang, B.

    2017-10-01

    Preliminary design of ITER Radial X-ray Camera (RXC) has been finished. The structure design is optimized and installation process is studied considering the simplification and easiness of maintenance. Remote handling procedures are designed for the system maintenance after being activated. For detector cooling against high environment temperature which can be up to 240°, a dedicated gas cooling system using heat exchanger is designed. The structure analysis indicates that the stresses and displacements of most of the components under load combinations are within the allowable limits and no Safety Important Component (SIC) boundary is damaged. Through putting B4C material in the front part of DSM and around detectors for neutron shielding, the detectors are expected to survive the whole D-D phase. As for electronics, preliminary design of highly integrated pre-amplifier and program controllable mid-amplifier has been completed, both with bandwidth greater than 100 kHz to meet time resolution requirement of 20 kHz. To protect the electronics from intensive neutron and gamma irradiation, shielding cabinet capable of attenuating neutron flux down to 0.0001 and gamma dose 0.01 is designed. Besides, many R&D has been done to support the design. The tests of pre-amplifier and mid-amplifier indicated the electronics had no functional problem when debugging together and generally passed preliminary ElectroMagnetic Compatibility (EMC) test and nuclear test. The highly-integrated compact pre-amplifier has been used in EAST and proved useful. To test the feasibility of dedicated gas cooling system for detectors, a cooling test platform was built and preliminary cooling test has been done, indicating that during 250°baking the detector temperature is promising to be cooled down to the detector temperature limit of 75°. To increase signal to noise ratio, large area detector with dark current less than 2nA has been manufactured and worked steadily in EAST experiments.

  14. Refraction and ultra-small-angle scattering of X-rays in a single-crystal diamond compound refractive lens.

    Science.gov (United States)

    Gasilov, S; Mittone, A; Dos Santos Rolo, T; Polyakov, S; Zholudev, S; Terentyev, S; Blank, V; Bravin, A; Baumbach, T

    2017-11-01

    In this work a double-crystal setup is employed to study compound refractive lenses made of single-crystal diamond. The point spread function of the lens is calculated taking into account the lens transmission, the wavefront aberrations, and the ultra-small-angle broadening of the X-ray beam. It is shown that, similarly to the wavefront aberrations, the ultra-small-angle scattering effects can significantly reduce the intensity gain and increase the focal spot size. The suggested approach can be particularly useful for the characterization of refractive X-ray lenses composed of many tens of unit lenses.

  15. The x-ray surface forces apparatus: Structure of a thin smectic liquid crystal film under confinement

    Energy Technology Data Exchange (ETDEWEB)

    Idziak, S.H.J.; Kraiser, K.E.; Safinya, C.R.; Warriner, H.E.; Hill, R.S.; Ruths, M.; Liang, K.S.; Israelachvili, J.N. (Univ. of California, Santa Barbara, CA (United States))

    1994-06-24

    An x-ray surface forces apparatus for simultaneously measuring forces and structures of confined complex fluids under static and flow conditions is described. This apparatus, combined with an intense synchrotron x-ray source, allows investigation of molecular orientations within a thin liquid crystal film confined between two shearing mica surfaces 3900 angstroms apart. The layer-forming smectic liquid crystal 8CB (4-cyano-4[prime]-octylbiphenyl) adopted a series of distinct planar layer orientations, including the bulk flow-forbidden b orientation.

  16. Demonstration of Single-Crystal Self-Seeded Two-Color X-Ray Free-Electron Lasers

    Energy Technology Data Exchange (ETDEWEB)

    Lutman, A. A.; Decker, F. -J; Arthur, J.; Chollet, M.; Feng, Y.; Hastings, J.; Huang, Z.; Lemke, H.; Nuhn, H. -D.; Marinelli, A.; Turner, J. L.; Wakatsuki, S.; Welch, J.; Zhu, D.

    2014-12-18

    A scheme for generating two simultaneous hard-x-ray free-electron laser pulses with a controllable difference in photon energy is described and then demonstrated using the self-seeding setup at the Linac Coherent Light Source (LCLS). The scheme takes advantage of the existing LCLS equipment, which allows two independent rotations of the self-seeding diamond crystal. The two degrees of freedom are used to select two nearby crystal reflections, causing two wavelengths to be present in the forward transmitted seeding x-ray pulse. The free-electron laser system must support amplification at both desired wavelengths.

  17. Pinhole X-ray Fluorescence Imaging of Gadolinium Nanoparticles: A Preliminary Monte Carlo Study

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Seong Moon; Sung, Won Mo; Ye, Sung Joon [Seoul National University, Seoul (Korea, Republic of)

    2014-10-15

    X-ray fluorescence imaging is a modality for the element-specific imaging of a subject through analysis of characteristic x-rays produced by exploiting the interaction of high atomic number elements and incoming x-rays. Previous studies have utilized a polychromatic x-ray source to investigate the production of in vivo x-ray fluorescence images for the assessment of concentrations and locations of gold nanoparticles. However, previous efforts have so far been unable to detect low concentrations, such as 0.001% gold by weight, which is an expected concentration accumulated in tumors. We examined the feasibility of a monochromatic synchrotron x-rays implementation of pinhole x-ray fluorescence imaging by Monte Carlo simulations using MCNP5. In the current study, gadolinium (Gd) nanoparticles, which have been widely used as a contrast agent in magnetic resonance imaging and also as a dose enhancer in radiation therapy, were chosen for tumor targeting. Since a monochromatic x-ray source is used, the increased x-ray fluorescence signals allow the detection of low concentrations of Gd. Two different monochromatic x-ray beam energies, 50.5 keV near the Kedge energy (i.e., 50.207 keV) of Gd and 55 keV, were compared by their respective imaging results. Using Monte Carlo simulations the feasibility of imaging low concentrations of Gd nanoparticles (e.g., 0.001 wt%) with x-ray fluorescence using monochromatic synchrotron x-rays of two different energies was shown. In the case of imaging a single Gd column inserted in the center of a water phantom, the fluorescence signals from 0.05 wt% and 0.1 wt% Gd columns irradiated with a 50.5 keV photon beam were higher than those irradiated with 55 keV. Below 0.05 wt% region no significant differences were found.

  18. Preliminary Research on Dual-Energy X-Ray Phase-Contrast Imaging

    OpenAIRE

    Han, Huajie; Wang, Shenghao; Gao, Kun; Wang, Zhili; Zhang, Can; Yang, Meng; Zhang, Kai; Zhu, Peiping

    2015-01-01

    Dual-energy X-ray absorptiometry (DEXA) has been widely applied to measure bone mineral density (BMD) and soft-tissue composition of human body. However, the use of DEXA is greatly limited for low-Z materials such as soft tissues due to their weak absorption. While X-ray phase-contrast imaging (XPCI) shows significantly improved contrast in comparison with the conventional standard absorption-based X-ray imaging for soft tissues. In this paper, we propose a novel X-ray phase-contrast method t...

  19. A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

    Science.gov (United States)

    Matsushita, Tadashi; Arakawa, Etsuo; Voegeli, Wolfgang; Yano, Yohko F.

    2013-01-01

    An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed. PMID:23254659

  20. Combining flat crystals, bent crystals and compound refractive lenses for high-energy X-ray optics.

    Science.gov (United States)

    Shastri, S D

    2004-03-01

    Compound refractive lenses (CRLs) are effective for collimating or focusing high-energy X-ray beams (50-100 keV) and can be used in conjunction with crystal optics in a variety of configurations, as demonstrated at the 1-ID undulator beamline of the Advanced Photon Source. As a primary example, this article describes the quadrupling of the output flux when a collimating CRL, composed of cylindrical holes in aluminium, is inserted between two successive monochromators, i.e. a modest-energy-resolution premonochromator followed by a high-resolution monochromator. The premonochromator is a cryogenically cooled divergence-preserving bent double-Laue Si(111) crystal device delivering an energy width DeltaE/E approximately 10(-3), which is sufficient for most experiments. The high-resolution monochromator is a four-reflection flat Si(111) crystal system resembling two channel-cuts in a dispersive arrangement, reducing the bandwidth to less than 10(-4), as required for some applications. Tests with 67 and 81 keV photon energies show that the high-resolution monochromator, having a narrow angular acceptance of a few microradians, exhibits a fourfold throughput enhancement due to the insertion of a CRL that reduces the premonochromatized beam's vertical divergence from 29 micro rad to a few microradians. The ability to focus high-energy X-rays with CRLs having long focal lengths (tens of meters) is also shown by creating a line focus of 70-90 micro m beam height in the beamline end-station with both the modest-energy-resolution and the high-energy-resolution monochromatic X-rays.

  1. Crystal structure of radium sulfate: An X-ray powder diffraction and density functional theory study

    Science.gov (United States)

    Matyskin, Artem V.; Ylmen, Rikard; Lagerkvist, Petra; Ramebäck, Henrik; Ekberg, Christian

    2017-09-01

    Radium-barium sulfate (Ra0.76Ba0.24SO4) powder was examined using X-ray Diffraction (XRD) technique and its crystal structure was optimized using Density Functional Theory (DFT). XRD data show that radium and barium sulfate form a solid solution and that Ra0.76Ba0.24SO4 is orthorhombic and isostructural with pure RaSO4, barite (BaSO4), celestite (SrSO4) and anglesite (PbSO4), crystallizing in the space group Pmna (No. 62). The unit cell parameters of the Ra0.76Ba0.24SO4 crystal have been determined using Rietveld refinement and were extrapolated to unit cell parameters of the pure RaSO4 phase using Vegard's law: a=9.129(8), b=5.538(3), c=7.313(5) Å. DFT geometry optimization was used to derive atomic coordinates and interatomic distances in both Ra0.76Ba0.24SO4 and pure RaSO4. The experimental and DFT geometry optimization results obtained in this work are in good agreement with each other, and furthermore with literature data.

  2. Single crystal X-ray diffraction studies of DNA and DNA-drug complexes

    CERN Document Server

    Todd, A K

    1999-01-01

    The structure of the brominated oligonucleotide d(ACGTACG(5-BrU)) sub 2 was solved using the multiwavelength anomalous diffraction (MAD) technique. The space group was P4 sub 3 2 sub 1 2, with unit cell a=b=43.60A, c=26.27A. This structure was an A-DNA, isomorphous with many other previously solved octomers. Single crystal X-ray diffraction data were collected from crystals of the intercalation complexes N-[2-(dimethylamino)ethyl] acridine-4-carboxamide (DACA), d(CGTACG) sub 2 and N-[2-(dimethylamino)ethyl] 9-aminoacridine-4-carboxamide (9- aminoDACA) and some of their derivatives. An attempt was made to solve the structure of the DACA derivative N-[2-(dimethylamino)butyl]-acridine-4-carboxamide (DACA4) by molecular replacement, using the crystal structure of the daunomycin d(CGTACG) sub 2 complex as a search model. Attempts were made to position the molecule in the unit cell based on an SIR map, knowledge of the symmetry and unit cell dimensions. The structure of the 9-amino-5-bromo DACA - d(CGT(5-BrU)CG) su...

  3. Upgrades of the high resolution imaging x-ray crystal spectrometers on experimental advanced superconducting tokamaka)

    Science.gov (United States)

    Lu, B.; Wang, F.; Shi, Y.; Bitter, M.; Hill, K. W.; Lee, S. G.; Fu, J.; Li, Y.; Wan, B.

    2012-10-01

    Two imaging x-ray crystal spectrometers, the so-called "poloidal" and "tangential" spectrometers, were recently implemented on experimental advanced superconducting tokamak (EAST) to provide spatially and temporally resolved impurity ion temperature (Ti), electron temperature (Te) and rotation velocity profiles. They are derived from Doppler width of W line for Ti, the intensity ratio of Li-like satellites to W line for Te, and Doppler shift of W line for rotation. Each spectrometer originally consisted of a spherically curved crystal and a two-dimensional multi-wire proportional counter (MWPC) detector. Both spectrometers have now been upgraded. The layout of the tangential spectrometer was modified, since it had to be moved to a different port, and the spectrometer was equipped with two high count rate Pilatus detectors (Model 100 K) to overcome the count rate limitation of the MWPC and to improve its time resolution. The poloidal spectrometer was equipped with two spherically bent crystals to record the spectra of He-like and H-like argon simultaneously and side by side on the original MWPC. These upgrades are described, and new results from the latest EAST experimental campaign are presented.

  4. Upgrades of the high resolution imaging x-ray crystal spectrometers on experimental advanced superconducting tokamak.

    Science.gov (United States)

    Lu, B; Wang, F; Shi, Y; Bitter, M; Hill, K W; Lee, S G; Fu, J; Li, Y; Wan, B

    2012-10-01

    Two imaging x-ray crystal spectrometers, the so-called "poloidal" and "tangential" spectrometers, were recently implemented on experimental advanced superconducting tokamak (EAST) to provide spatially and temporally resolved impurity ion temperature (T(i)), electron temperature (T(e)) and rotation velocity profiles. They are derived from Doppler width of W line for Ti, the intensity ratio of Li-like satellites to W line for Te, and Doppler shift of W line for rotation. Each spectrometer originally consisted of a spherically curved crystal and a two-dimensional multi-wire proportional counter (MWPC) detector. Both spectrometers have now been upgraded. The layout of the tangential spectrometer was modified, since it had to be moved to a different port, and the spectrometer was equipped with two high count rate Pilatus detectors (Model 100 K) to overcome the count rate limitation of the MWPC and to improve its time resolution. The poloidal spectrometer was equipped with two spherically bent crystals to record the spectra of He-like and H-like argon simultaneously and side by side on the original MWPC. These upgrades are described, and new results from the latest EAST experimental campaign are presented.

  5. Indentation Size Effects in Single Crystal Copper as Revealed by Synchrotron X-ray Microdiffraction

    Energy Technology Data Exchange (ETDEWEB)

    Feng, G.; Budiman, A. S.; Nix, W. D.; Tamura, N.; Patel, J. R.

    2007-11-19

    The indentation size effect (ISE) has been observed in numerous nanoindentation studies on crystalline materials; it is found that the hardness increases dramatically with decreasing indentation size - a 'smaller is stronger' phenomenon. Some have attributed the ISE to the existence of strain gradients and the geometrically necessary dislocations (GNDs). Since the GND density is directly related to the local lattice curvature, the Scanning X-ray Microdiffraction ({mu}SXRD) technique, which can quantitatively measure relative lattice rotations through the streaking of Laue diffractions, can used to study the strain gradients. The synchrotron {mu}SXRD technique we use - which was developed at the Advanced Light Source (ALS), Berkeley Lab - allows for probing the local plastic behavior of crystals with sub-micrometer resolution. Using this technique, we studied the local plasticity for indentations of different depths in a Cu single crystal. Broadening of Laue diffractions (streaking) was observed, showing local crystal lattice rotation due to the indentation-induced plastic deformation. A quantitative analysis of the streaking allows us to estimate the average GND density in the indentation plastic zones. The size dependence of the hardness, as found by nanoindentation, will be described, and its correlation to the observed lattice rotations will be discussed.

  6. X-ray diffraction of protein crystal grown in a nano-liter scale droplet in a microchannel and evaluation of its applicability.

    Science.gov (United States)

    Maeki, Masatoshi; Yoshizuka, Saori; Yamaguchi, Hiroshi; Kawamoto, Masahide; Yamashita, Kenichi; Nakamura, Hiroyuki; Miyazaki, Masaya; Maeda, Hideaki

    2012-01-01

    We describe the technical aspects of the in-situ X-ray diffraction of a protein crystal prepared by a nanodroplet-based crystallization method. We were able to obtain diffraction patterns from a crystal grown in a capillary without any manipulation. Especially in our experimental approach, the crystals that moved to the nanodroplet interface were fixed strongly enough to carry out X-ray diffraction measurements that could be attributed to the high surface tension of the nanodroplet. The crystal was damaged by an indirect action of the X-rays because our in-situ X-ray diffraction measurement was carried out in the liquid phase without freezing the crystal; however, the obtained several diffraction patterns were of sufficiently fine quality for the crystal structure factors to be generated. We consider the technical examination presented in this paper to represent a seamless coupling of crystallization to X-ray analysis.

  7. Optical features of a LiF crystal soft X-ray imaging detector irradiated by free electron laser pulses.

    Science.gov (United States)

    Pikuz, Tatiana; Faenov, Anatoly; Fukuda, Yuji; Kando, Masaki; Bolton, Paul; Mitrofanov, Alexander; Vinogradov, Alexander; Nagasono, Mitsuru; Ohashi, Haruhiko; Yabashi, Makina; Tono, Kensuke; Senba, Yashinori; Togashi, Tadashi; Ishikawa, Tetsuya

    2012-02-13

    Optical features of point defects photoluminescence in LiF crystals, irradiated by soft X-ray pulses of the Free Electron Laser with wavelengths of 17.2 - 61.5 nm, were measured. We found that peak of photoluminescence spectra lies near of 530 nm and are associated with emission of F3+ centers. Our results suggest that redistribution of photoluminescence peak intensity from the red to the green part of the spectra is associated with a shortening of the applied laser pulses down to pico - or femtosecond durations. Dependence of peak intensity of photoluminescence spectra from the soft X-ray irradiation fluence was measured and the absence of quenching phenomena, even at relatively high fluencies was found, which is very important for wide applications of LiF crystal X-ray imaging detectors.

  8. High Resolution X-ray Characterization Of Mosaic Crystals For Hard X- And Gamma-ray Astronomy

    Science.gov (United States)

    Marchini, L.; Ferrari, C.; Buffagni, E.; Zappettini, A.

    2011-09-01

    For hard X-ray astronomy in the 70-1000 keV energy range Laue lenses have been proposed where the focusing elements are made of single mosaic crystals, in order to increase the diffraction efficiency with respect to perfect crystals. Suitable crystals to be used for such application should have a sufficient density to increase the diffraction efficiency and a mosaicity ranging between 30 arcsec and 1-2 arcmin, depending on the lens focusing distance and resolution. In the past germanium and copper crystals, often employed as monochromators for neutrons, have been considered. In this work we propose several crystalline materials of different degree of crystal perfection such as GaAs, Cu, CdTe, and CdZnTe as possible mosaic crystals for hard X-ray astronomy. They were analyzed by high resolution X-ray diffraction at 8 keV and by diffraction at energies up to 700 keV at synchrotron. It was found that: CdTe and CdZnTe crystals exhibit low angle grain boundaries preventing the formation of a single diffracted X-ray beam; Cu crystals exhibit mosaicity of the order of several arcmin, however a deep etching is needed to remove the cutting damage; GaAs crystals grown by LEC method show mosaicity between 15 and 30 arcsec and good diffraction efficiency up to energies of 700 keV. Annealing and surface damage were considered as possible methods to increase the GaAs crystal mosaicity.

  9. Curved crystal x-ray optics for monochromatic imaging with a clinical source.

    Science.gov (United States)

    Bingölbali, Ayhan; MacDonald, C A

    2009-04-01

    Monochromatic x-ray imaging has been shown to increase contrast and reduce dose relative to conventional broadband imaging. However, clinical sources with very narrow energy bandwidth tend to have limited intensity and field of view. In this study, focused fan beam monochromatic radiation was obtained using doubly curved monochromator crystals. While these optics have been in use for microanalysis at synchrotron facilities for some time, this work is the first investigation of the potential application of curved crystal optics to clinical sources for medical imaging. The optics could be used with a variety of clinical sources for monochromatic slot scan imaging. The intensity was assessed and the resolution of the focused beam was measured using a knife-edge technique. A simulation model was developed and comparisons to the measured resolution were performed to verify the accuracy of the simulation to predict resolution for different conventional sources. A simple geometrical calculation was also developed. The measured, simulated, and calculated resolutions agreed well. Adequate resolution and intensity for mammography were predicted for appropriate source/optic combinations.

  10. Processing of X-ray snapshots from crystals in random orientations.

    Science.gov (United States)

    Kabsch, Wolfgang

    2014-08-01

    A functional expression is introduced that relates scattered X-ray intensities from a still or a rotation snapshot to the corresponding structure-factor amplitudes. The new approach was implemented in the program nXDS for processing monochromatic diffraction images recorded by a multi-segment detector where each exposure could come from a different crystal. For images containing indexable spots, the intensities of the expected reflections and their variances are obtained by profile fitting after mapping the contributing pixel contents to the Ewald sphere. The varying intensity decline owing to the angular distance of the reflection from the surface of the Ewald sphere is estimated using a Gaussian rocking curve. This decline is dubbed `Ewald offset correction', which is well defined even for still images. Together with an image-scaling factor and other corrections, an explicit expression is defined that predicts each recorded intensity from its corresponding structure-factor amplitude. All diffraction parameters, scaling and correction factors are improved by post-refinement. The ambiguous case of a lower point group than the lattice symmetry is resolved by a method reminiscent of the technique of `selective breeding'. It selects the indexing alternative for each image that yields, on average, the highest correlation with intensities from all other images. Processing a test set of rotation images by XDS and treating the same images by nXDS as snapshots of crystals in random orientations yields data of comparable quality, clearly indicating an anomalous signal from Se atoms.

  11. Crystal engineering on industrial diaryl pigments using lattice energy minimizations and X-ray powder diffraction.

    Science.gov (United States)

    Schmidt, Martin U; Dinnebier, Robert E; Kalkhof, Holger

    2007-08-23

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  12. An optimal strategy for X-ray data collection on macromolecular crystals with position-sensitive detectors

    NARCIS (Netherlands)

    Vicković, Ivan; Kalk, Kor H.; Drenth, Jan; Dijkstra, Bauke W.

    1994-01-01

    X-ray data collection on macromolecular crystals is preferably done with minimum exposure time and high completeness. A Fortran procedure - DCS - has been written in the environment of the MADNES program to predict the completeness of data before the start of actual data collection. In addition, the

  13. The first X-ray crystal structure of the glucocorticoid receptor bound to a non-steroidal agonist

    Energy Technology Data Exchange (ETDEWEB)

    Madauss, Kevin P.; Bledsoe, Randy K.; Mclay, Iain; Stewart, Eugene L.; Uings, Iain J.; Weingarten, Gordon; Williams, Shawn P. (GSKNC); (GSK)

    2009-07-23

    The amino-pyrazole 2,6-dichloro-N-ethyl benzamide 1 is a selective GR agonist with dexamethasone-like in vitro potency. Its X-ray crystal structure in the GR LBD (Glucocorticoid ligand-binding domain) is described and compared to other reported structures of steroidal GR agonists in the GR LBD (3E7C).

  14. A United Effort for Crystal Growth, Neutron Scattering, and X-ray Scattering Studies of Novel Correlated Electron Materials

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young S. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2015-02-12

    The research accomplishments during the award involved experimental studies of correlated electron systems and quantum magnetism. The techniques of crystal growth, neutron scattering, x-ray scattering, and thermodynamic & transport measurements were employed, and graduate students and postdoctoral research associates were trained in these techniques.

  15. X-ray diffraction study with small- and wide-angle simultaneous measurement of polymorphic crystallization of triacylglycerols

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, Satoru [Hiroshima Univ., Faculty of Applied Biological Science, Higashi-Hiroshima, Hiroshima (Japan)

    2002-01-01

    Polymorphism of triacylglycerols (TAGs) is an important phenomenon which influences the physical chemical properties of fats employed in foods, pharmaceuticals, cosmetics etc. In particular, precise analysis of kinetic properties of polymorphic crystallization is closely related to technical control of fat crystallization in confectionery and food industry. In the melt-mediated crystallization, which is one of the typical methods of crystallizing the more stable form for industrial use, the more stable form is induced by rapidly melting the less stable forms. Recently, X-ray diffraction spectroscopy using a synchrotron radiation source has been used in study of dynamic processes of polymorphic transformations of many TAGs. This approach has allowed us to gain a better understanding of the kinetics of processes occurring during the polymorphic crystallization and transformations of TAGs at the molecular level. In the present study, polymorphic crystallization of TAG has been examined with the time-resolved X-ray diffraction method with small- and wide-angle simultaneous measurement using synchrotron radiation. The main result is as follows: the melt mediation gave rise to the formation of a liquid crystalline structure having long spacing values of 5.1 nm and 4.6 nm in SOS (sn-1,3-distearoyl-2-oleoyl glycerol). Consequently, the use of the time-resolved X-ray diffraction method with small- and wide-angle simultaneous measurement using synchrotron radiation unveiled quite newer aspects of the polymorphic crystallization of the triacylglycerols from neat liquid, which were not detectable in conventional XRD techniques. (author)

  16. Extreme UV and X-ray scattering measurements from a rough LiF crystal surface characterized by electron micrography

    DEFF Research Database (Denmark)

    Alehyane; Arbaoui; Barchewitz

    1989-01-01

    XUV and X-ray scattering by a LiF crystal is measured. The angular distribution of the scattered radiation (ADSR) reveals characteristic features, side peaks or asymmetry. The surface of the sample is statistically characterized by a microdensitometer analysis of electron micrographs resolving...... of the ADSR features in terms of the modulation of the surface power spectral density function associated with the microroughness by an optical factor. The possibility of obtaining short scale roughness characterization from XUV or X-ray measurements is discussed...

  17. Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Olfa Mtioui-Sghaier

    2015-07-01

    Full Text Available The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005. Eur. J. Inorg. Chem. pp. 3080–3087; Cavalcante et al. (2013. Polyhedron, 54, 13–25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octahedra, both with point group symmetry 2. The distortion of the octahedra is reflected by variation of bond lengths and angles from 2.002 (3–2.274 (4 Å, 80.63 (11–108.8 (2° for equatorial and 158.4 (2– 162.81 (14° for axial angles (ZnO6, and of 1.769 (3–2.171 (3 Å, 73.39 (16–104.7 (2, 150.8 (2–164.89 (15° (MoO6, respectively. In the crystal structure, the same type of MO6 octahedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexagonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octahedral voids.

  18. Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

    Science.gov (United States)

    Baba, Seiki; Hoshino, Takeshi; Ito, Len; Kumasaka, Takashi

    2013-01-01

    Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection. PMID:23999307

  19. Measurement of trace elements in KH/sub 2/PO/sub 4/ crystals by x-ray fluorescence spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Ryon, R.W.; Duewer, T.I.

    1981-02-01

    A non-destructive method is described for the quantitative measurement of impurities in KDP (KH/sub 2/PO/sub 4/) crystals. Part per million concentrations of impurities can be determined with good accuracy in about one hour of instrument time. An energy dispersive x-ray spectrometer is used. Both the crystals and the solutions from which they are grown may be analyzed.

  20. A doubly curved elliptical crystal spectrometer for the study of localized x-ray absorption in hot plasmas.

    Science.gov (United States)

    Cahill, Adam D; Hoyt, Cad L; Pikuz, Sergei A; Shelkovenko, Tania; Hammer, David A

    2014-10-01

    X-ray absorption spectroscopy is a powerful tool for the diagnosis of plasmas over a wide range of both temperature and density. However, such a measurement is often limited to probing plasmas with temperatures well below that of the x-ray source in order to avoid object plasma emission lines from obscuring important features of the absorption spectrum. This has excluded many plasmas from being investigated by this technique. We have developed an x-ray spectrometer that provides the ability to record absorption spectra from higher temperature plasmas than the usual approach allows without the risk of data contamination by line radiation emitted by the plasma under study. This is accomplished using a doubly curved mica crystal which is bent both elliptically and cylindrically. We present here the foundational work in the design and development of this spectrometer along with initial results obtained with an aluminum x-pinch as the object plasma.

  1. Diagnosis of a two wire X-pinch by X-ray absorption spectroscopy utilizing a doubly curved ellipsoidal crystal

    Energy Technology Data Exchange (ETDEWEB)

    Cahill, A. D., E-mail: adc87@cornell.edu; Hoyt, C. L., E-mail: adc87@cornell.edu; Shelkovenko, T. A., E-mail: adc87@cornell.edu; Pikuz, S. A., E-mail: adc87@cornell.edu; Hammer, D. A., E-mail: adc87@cornell.edu [Cornell University, 439 Rhodes Hall, Ithaca, NY 14853 (United States)

    2014-12-15

    X-ray absorption spectroscopy is a powerful tool for the diagnosis of plasmas over a wide range of both temperature and density. However, such a measurement is often limited to probing plasmas with temperatures well below that of the x-ray source in order to avoid object plasma emission lines from obscuring important features of the absorption spectrum. This has excluded many plasmas from being investigated by this technique. We have developed an x-ray spectrometer that provides the ability to record absorption spectra from higher temperature plasmas than the usual approach allows without the risk of data contamination by line radiation emitted by the plasma under study. This is accomplished using a doubly curved mica crystal which is bent both elliptically and cylindrically. We present here initial absorption spectra obtained from an aluminum x-pinch plasma.

  2. A doubly curved elliptical crystal spectrometer for the study of localized x-ray absorption in hot plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Cahill, Adam D., E-mail: adc87@cornell.edu; Hoyt, Cad L.; Pikuz, Sergei A.; Shelkovenko, Tania; Hammer, David A. [Cornell University, Electrical and Computer Engineering, Ithaca, NY 14853 (United States)

    2014-10-15

    X-ray absorption spectroscopy is a powerful tool for the diagnosis of plasmas over a wide range of both temperature and density. However, such a measurement is often limited to probing plasmas with temperatures well below that of the x-ray source in order to avoid object plasma emission lines from obscuring important features of the absorption spectrum. This has excluded many plasmas from being investigated by this technique. We have developed an x-ray spectrometer that provides the ability to record absorption spectra from higher temperature plasmas than the usual approach allows without the risk of data contamination by line radiation emitted by the plasma under study. This is accomplished using a doubly curved mica crystal which is bent both elliptically and cylindrically. We present here the foundational work in the design and development of this spectrometer along with initial results obtained with an aluminum x-pinch as the object plasma.

  3. Monte Carlo simulation applied in total reflection x-ray fluorescence: Preliminary results

    Energy Technology Data Exchange (ETDEWEB)

    Meira, Luiza L. C.; Inocente, Guilherme F.; Vieira, Leticia D.; Mesa, Joel [Departamento de Fisica e Biofisica - Instituto de Biociencias de Botucatu, Universidade Estadual Paulista Julio de Mesquita Filho (Brazil)

    2013-05-06

    The X-ray Fluorescence (XRF) analysis is a technique for the qualitative and quantitative determination of chemical constituents in a sample. This method is based on detection of the characteristic radiation intensities emitted by the elements of the sample, when properly excited. A variant of this technique is the Total Reflection X-ray Fluorescence (TXRF) that utilizes electromagnetic radiation as excitation source. In total reflection of X-ray, the angle of refraction of the incident beam tends to zero and the refracted beam is tangent to the sample support interface. Thus, there is a minimum angle of incidence at which no refracted beam exists and all incident radiation undergoes total reflection. In this study, we evaluated the influence of the energy variation of the beam of incident x-rays, using the MCNPX code (Monte Carlo NParticle) based on Monte Carlo method.

  4. Crystallization and X-ray diffraction studies of cellobiose phosphorylase from Cellulomonas uda.

    Science.gov (United States)

    Van Hoorebeke, Annelies; Stout, Jan; Kyndt, John; De Groeve, Manu; Dix, Ina; Desmet, Tom; Soetaert, Wim; Van Beeumen, Jozef; Savvides, Savvas N

    2010-03-01

    Disaccharide phosphorylases are able to catalyze both the synthesis and the breakdown of disaccharides and have thus emerged as attractive platforms for tailor-made sugar synthesis. Cellobiose phosphorylase from Cellulomonas uda (CPCuda) is an enzyme that belongs to glycoside hydrolase family 94 and catalyzes the reversible breakdown of cellobiose [beta-D-glucopyranosyl-(1,4)-D-glucopyranose] to alpha-D-glucose-1-phosphate and D-glucose. Crystals of ligand-free recombinant CPCuda and of its complexes with substrates and reaction products yielded complete X-ray diffraction data sets to high resolution using synchrotron radiation but suffered from significant variability in diffraction quality. In at least one case an intriguing space-group transition from a primitive monoclinic to a primitive orthorhombic lattice was observed during data collection. The structure of CPCuda was determined by maximum-likelihood molecular replacement, thus establishing a starting point for an investigation of the structural and mechanistic determinants of disaccharide phosphorylase activity.

  5. X-ray crystal structure of the fibrinolysis inhibitor [alpha][subscript 2]-antiplasmin

    Energy Technology Data Exchange (ETDEWEB)

    Law, Ruby H.P.; Sofian, Trifina; Kan, Wan-Ting; Horvath, Anita J.; Hitchen, Corinne R.; Langendorf, Christopher G.; Buckle, Ashley M.; Whisstock, James C.; Coughlin, Paul B. (Monash)

    2008-12-11

    The serpin alpha(2)-antiplasmin (SERPINF2) is the principal inhibitor of plasmin and inhibits fibrinolysis. Accordingly, alpha(2)-antiplasmin deficiency in humans results in uncontrolled fibrinolysis and a bleeding disorder. alpha(2)-antiplasmin is an unusual serpin, in that it contains extensive N- and C-terminal sequences flanking the serpin domain. The N-terminal sequence is crosslinked to fibrin by factor XIIIa, whereas the C-terminal region mediates the initial interaction with plasmin. To understand how this may happen, we have determined the 2.65A X-ray crystal structure of an N-terminal truncated murine alpha(2)-antiplasmin. The structure reveals that part of the C-terminal sequence is tightly associated with the body of the serpin. This would be anticipated to position the flexible plasmin-binding portion of the C-terminus in close proximity to the serpin Reactive Center Loop where it may act as a template to accelerate serpin/protease interactions.

  6. Stable anilinyl radicals coordinated to nickel: X-ray crystal structure and characterization.

    Science.gov (United States)

    Kochem, Amélie; Gellon, Gisèle; Leconte, Nicolas; Baptiste, Benoit; Philouze, Christian; Jarjayes, Olivier; Orio, Maylis; Thomas, Fabrice

    2013-12-02

    Two anilinosalen and a mixed phenol-anilinosalen ligands involving sterically hindered anilines moieties were synthesized. Their nickel(II) complexes 1, 2, and 3 were prepared and characterized. They could be readily one-electron oxidized (E(1/2)=-0.30, -0.26 and 0.10 V vs. Fc(+)/Fc, respectively) into anilinyl radicals species [1](+), [2](+), and [3](+), respectively. The radical complexes are extremely stable and were isolated as single crystals. X-ray crystallographic structures reveal that the changes in bond length resulting from oxidation do not exceed 0.02 Å within the ligand framework in the symmetrical [1](+) and [2](+). No quinoid bond pattern was present. In contrast, larger structural rearrangements were evidenced for the unsymmetrical [3](+), with shortening of one C(ortho)-C(meta) bond. Radical species [1](+) and [2](+) exhibit a strong absorption band at around 6000 cm(-1) (class III mixed valence compounds). This band is significantly less intense than [3](+), consistent with a rather localized anilinyl radical character, and thus a classification of this species as class II mixed-valence compound. Magnetic and electronic properties, as well as structural parameters, have been computed by DFT methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Momentum-resolved resonant inelastic X-ray scattering on a single crystal under high pressure.

    Science.gov (United States)

    Yoshida, Masahiro; Ishii, Kenji; Jarrige, Ignace; Watanuki, Tetsu; Kudo, Kazutaka; Koike, Yoji; Kumagai, Ken'ichi; Hiraoka, Nozomu; Ishii, Hirofumi; Tsuei, Ku-Ding; Mizuki, Jun'ichiro

    2014-01-01

    A single-crystal momentum-resolved resonant inelastic X-ray scattering (RIXS) experiment under high pressure using an originally designed diamond anvil cell (DAC) is reported. The diamond-in/diamond-out geometry was adopted with both the incident and scattered beams passing through a 1 mm-thick diamond. This enabled us to cover wide momentum space keeping the scattering angle condition near 90°. Elastic and inelastic scattering from the diamond was drastically reduced using a pinhole placed after the DAC. Measurement of the momentum-resolved RIXS spectra of Sr2.5Ca11.5Cu24O41 at the Cu K-edge was thus successful. Though the inelastic intensity becomes weaker by two orders than the ambient pressure, RIXS spectra both at the center and the edge of the Brillouin zone were obtained at 3 GPa and low-energy electronic excitations of the cuprate were found to change with pressure.

  8. X-ray crystal structure of embelin and its DFT scavenging of superoxide radical.

    Science.gov (United States)

    Caruso, Francesco; Paumier, Sarah; Rossi, Miriam

    2017-08-28

    Embelin is a phytochemical component of tropical plants that have a long history of being used in ethnic pharmacology in various parts of the world, including Ayurdvedic and Chinese medicinal texts. Many modern studies confirm its promise as a medicinal compound. The X-ray crystal structure determination of embelin shows a remarkably ordered alkyl chain and particularly strong pi-pi interactions for a nonaromatic system. The molecule has a torsion angle of 67° between the ring and the alkyl chain of the molecule and differs markedly from that seen when embelin is embedded in the plasminogen activator inhibitor-1 (PAI-1) binding site (almost planar-with about 10° torsion angle). This suggests that embelin's flexible structural skeleton can be useful in biological environment. Apart from this, its many biological activities likely depend on embelin's hydrophobic nonpolar tail that allows a variety of interactions. Computationally, we evaluated embelin's sequestering ability toward the superoxide radical and see that embelin executes this reaction in a novel manner. Namely, as shown by our DFT calculations, instead of releasing a H atom to the superoxide radical to form the anionic species O2 H- , embelin prefers to accept an electron from the superoxide radical, which then transforms into molecular oxygen, O2 . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  9. Complete polarization analysis of high energy soft x-rays by combining a multilayer phase retarder with crystal analyzer

    Science.gov (United States)

    Wang, H.; Dhesi, S. S.; Maccherozzi, F.; Sawhney, K. J. S.

    2012-06-01

    We demonstrate a complete polarization analysis of soft x-rays with an energy of 1.1 keV using a free-standing W/B4C multilayer phase retarders and a beryl crystal analyzer. The W/B4C multilayer exhibits five times increase in transmission over that previously reported. The beryl crystal proves to be a suitable analyzer for the polarization analysis with a 10% s-component of reflectivity resulting in an extinction ratio close to 0.002 at 1.1 keV. The combination of multilayer phase retarders and crystal analyzers should open up the field of the soft x-ray polarization analysis in the energy range between 1 keV and 2 keV.

  10. Mapping of Lattice Strain in 4H-SiC Crystals by Synchrotron Double-Crystal X-ray Topography

    Science.gov (United States)

    Guo, Jianqiu; Yang, Yu; Raghothamachar, Balaji; Dudley, Michael; Stoupin, Stanislav

    2018-02-01

    The presence of lattice strain in n-doped 4H-SiC substrate crystals grown by a physical vapor transport method can strongly influence the performance of related power devices that are fabricated on them. Information on the level and the variation of lattice strain in these wafer crystals is thus important. In this study, a non-destructive method is developed based on synchrotron double-crystal x-ray topography to map lattice strains in 4H-SiC wafers. Measurements are made on two 4H-SiC substrate crystals—one is an unprocessed commercial wafer while the other was subject to a post-growth high-temperature heat treatment. Maps of different strain components are generated from the equi-misorientation contour maps recorded using synchrotron monochromatic radiation. The technique is demonstrated to be a powerful tool in estimating strain fields in 4H-SiC crystals. Analysis of the strain maps also shows that the normal strain components vary much more significantly than do the shear/rotation components, indicating that lattice dilation/compression rather than lattice tilt is the major type of deformation caused by both the incorporation of nitrogen dopants and the nucleation of basal plane dislocations.

  11. Mapping of Lattice Strain in 4H-SiC Crystals by Synchrotron Double-Crystal X-ray Topography

    Science.gov (United States)

    Guo, Jianqiu; Yang, Yu; Raghothamachar, Balaji; Dudley, Michael; Stoupin, Stanislav

    2017-09-01

    The presence of lattice strain in n-doped 4H-SiC substrate crystals grown by a physical vapor transport method can strongly influence the performance of related power devices that are fabricated on them. Information on the level and the variation of lattice strain in these wafer crystals is thus important. In this study, a non-destructive method is developed based on synchrotron double-crystal x-ray topography to map lattice strains in 4H-SiC wafers. Measurements are made on two 4H-SiC substrate crystals—one is an unprocessed commercial wafer while the other was subject to a post-growth high-temperature heat treatment. Maps of different strain components are generated from the equi-misorientation contour maps recorded using synchrotron monochromatic radiation. The technique is demonstrated to be a powerful tool in estimating strain fields in 4H-SiC crystals. Analysis of the strain maps also shows that the normal strain components vary much more significantly than do the shear/rotation components, indicating that lattice dilation/compression rather than lattice tilt is the major type of deformation caused by both the incorporation of nitrogen dopants and the nucleation of basal plane dislocations.

  12. Synchrotron radiation X-ray tomographic microscopy (SRXTM of brachiopod shell interiors for taxonomy: Preliminary report

    Directory of Open Access Journals (Sweden)

    Motchurova-Dekova Neda

    2010-01-01

    Full Text Available Synchrotron radiation X-ray tomographic microscopy (SRXTM is a non-destructive technique for the investigation and visualization of the internal features of solid opaque objects, which allows reconstruction of a complete three-dimensional image of internal structures by recording of the differences in the effects on the passage of waves of energy reacting with those structures. Contrary to X-rays, produced in a conventional X-ray tube, the intense synchrotron light beams are sharply focused like a laser beam. We report encouraging results from the use of SRXTM for purely taxonomic purposes in brachiopods: an attempt to find a non-destructive and more efficient alternative to serial sectioning and several other methods of dissection together with the non-destructive method of X-ray computerised micro-tomography. Two brachiopod samples were investigated using SRXTM. In “Rhynchonella” flustracea it was possible to visualise the 3D shape of the crura and dental plates. In Terebratulina imbricata it was possible to reveal the form of the brachidium. It is encouraging that we have obtained such promising results using SRXTM with our very first two fortuitous samples, which had respectively fine-grained limestone and marl as infilling sediment, in contrast to the discouraging results communicated to us by some colleagues who have tested specimens with such infillings using X-ray micro-tomography. In future the holotypes, rare museum specimens or delicate Recent material may be preferentially subjected to this mode of analysis.

  13. Contact X-ray microscopy of living cells by using LiF crystal as imaging detector.

    Science.gov (United States)

    Reale, L; Bonfigli, F; Lai, A; Flora, F; Albertano, P; DI Giorgio, M L; Mezi, L; Montereali, R M; Faenov, A; Pikuz, T; Almaviva, S; Francucci, M; Gaudio, P; Martellucci, S; Richetta, M; Poma, A

    2015-05-01

    In this paper, the use of lithium fluoride (LiF) as imaging radiation detector to analyse living cells by single-shot soft X-ray contact microscopy is presented. High resolved X-ray images on LiF of cyanobacterium Leptolyngbya VRUC135, two unicellular microalgae of the genus Chlamydomonas and mouse macrophage cells (line RAW 264.7) have been obtained utilizing X-ray radiation in the water window energy range from a laser plasma source. The used method is based on loading of the samples, the cell suspension, in a special holder where they are in close contact with a LiF crystal solid-state X-ray imaging detector. After exposure and sample removal, the images stored in LiF by the soft X-ray contact microscopy technique are read by an optical microscope in fluorescence mode. The clear image of the mucilaginous sheath the structure of the filamentous Leptolyngbya and the visible nucleolus in the macrophage cells image, are noteworthiness results. The peculiarities of the used X-ray radiation and of the LiF imaging detector allow obtaining images in absorption contrast revealing the internal structures of the investigated samples at high spatial resolution. Moreover, the wide dynamic range of the LiF imaging detector contributes to obtain high-quality images. In particular, we demonstrate that this peculiar characteristic of LiF detector allows enhancing the contrast and reveal details even when they were obscured by a nonuniform stray light. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  14. Insect-cell expression, crystallization and X-ray data collection of the bradyzoite-specific antigen BSR4 from Toxoplasma gondii

    Energy Technology Data Exchange (ETDEWEB)

    Grujic, Ognjen [Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, V8W 3P6 (Canada); Grigg, Michael E. [Molecular Parasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Center Drive, Bethesda, MD 20892 (United States); Boulanger, Martin J., E-mail: mboulang@uvic.ca [Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, V8W 3P6 (Canada)

    2008-05-01

    Preliminary X-ray diffraction studies of the bradyzoite-specific surface antigen BSR4 from T. gondii are described. Toxoplasma gondii is an important global pathogen that infects nearly one third of the world’s adult population. A family of developmentally expressed structurally related surface-glycoprotein adhesins (SRSs) mediate attachment to and are utilized for entry into host cells. The latent bradyzoite form of T. gondii persists for the life of the host and expresses a distinct family of SRS proteins, of which the bradyzoite-specific antigen BSR4 is a prototypical member. Structural studies of BSR4 were initiated by first recombinantly expressing BSR4 in insect cells, which was followed by crystallization and preliminary X-ray data collection to 1.95 Å resolution. Data processing showed that BSR4 crystallized with one molecule in the asymmetric unit of the P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2 space group, with a solvent content of 60% and a corresponding Matthews coefficient of 2.98 Å{sup 3} Da{sup −1}.

  15. Collimating Montel mirror as part of a multi-crystal analyzer system for resonant inelastic X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jungho; Shi, Xianbo; Casa, Diego; Qian, Jun; Huang, XianRong; Gog, Thomas

    2016-06-01

    Advances in resonant inelastic X-ray scattering (RIXS) have come in lockstep with improvements in energy resolution. Currently, the best energy resolution at the IrL3-edge stands at ~25 meV, which is achieved using a diced Si(844) spherical crystal analyzer. However, spherical analyzers are limited by their intrinsic reflection width. A novel analyzer system using multiple flat crystals provides a promising way to overcome this limitation. For the present design, an energy resolution at or below 10 meV was selected. Recognizing that the angular acceptance of flat crystals is severely limited, a collimating element is essential to achieve the necessary solid-angle acceptance. For this purpose, a laterally graded, parabolic, multilayer Montel mirror was designed for use at the IrL3-absorption edge. It provides an acceptance larger than 10 mrad, collimating the reflected X-ray beam to smaller than 100 µrad, in both vertical and horizontal directions. The performance of this mirror was studied at beamline 27-ID at the Advanced Photon Source. X-rays from a diamond (111) monochromator illuminated a scattering source of diameter 5 µm, generating an incident beam on the mirror with a well determined divergence of 40 mrad. A flat Si(111) crystal after the mirror served as the divergence analyzer. From X-ray measurements, ray-tracing simulations and optical metrology results, it was established that the Montel mirror satisfied the specifications of angular acceptance and collimation quality necessary for a high-resolution RIXS multi-crystal analyzer system.

  16. LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

    Energy Technology Data Exchange (ETDEWEB)

    Kusakizako, Tsukasa [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Tanaka, Yoshiki [Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 (Japan); Hipolito, Christopher J. [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575 (Japan); Kuroda, Teruo [Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 (Japan); Ishitani, Ryuichiro [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Suga, Hiroaki [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)

    2016-06-22

    A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-ray diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.

  17. Animated simulation of the paths of X-ray wave fields in a crystal containing a dislocation : Spherical incident wave

    OpenAIRE

    Epelboin, Yves; Guidi-Morosini, Christian; Morris, François; Rimsky, Alexandre; Soyer, Alain

    1987-01-01

    The propagation of X-ray wave fields in a crystal containing a dislocation is computed according to the dynamical theory and the intensities inside the crystal are represented in false colours. The position of the core of the dislocation is represented by a white cross. The video illustrate the case of an incident spherical wave on a Silicon crystal 400 micron thick , reflection (3 3 -3) with Mo Kalpha radiation (Bragg angle 19.83 degrees). Increasing intensities are visualized with the follo...

  18. Bent Crystals By Superficial Grooves For High-efficiency Concentration Of Hard X-ray Photons By A Laue Lens

    Science.gov (United States)

    Guidi, V.; Bellucci, V.; Camattari, R.; Neri, I.

    2011-09-01

    We propose a technique to fabricate self-standing curved crystals for high-efficiency concentration of hard X-ray photons by a Laue lens. This technique relies on superficial grooves on a mono- crystal by a diamond saw. Extension of the method to materials with higher atomic number, e.g., Ge, has been undertaken to provide high-efficiency diffraction up to 800 keV. With respect to other proposed techniques, the method of indentations is cheap, simple and reproducible, being based on mass production tools. It is possible to use curved crystal in two different geometries. Employing the ``geometry one'', it is possible to exploit the curvature directly imparted to the crystal to achieve high-efficiency diffraction. Grooved Si crystals were characterized in this geometry at ESRF and efficiently diffracted up to 500 keV, peaking 95% at 150 keV. The ``geometry two'' consists in exploiting the so-called quasi-mosaicity to obtain high-resolution focusing of X-rays. As a result of primary curvature imparted to the crystal, a secondary curvature (Quasi-Mosaic curvature) occurs. We demonstrated that a combination of primary and quasi-mosaic curvatures allows high-efficiency diffraction and high-resolution focusing of diffracted photons. Quasi-Mosaic crystals would increases the signal-to-noise ratio of about one orders of magnitude with respect to mosaic crystals and no mosaic defocusing would occur.

  19. Study of the crystallization kinetics of LAS glass by differential scanning calorimetry, X-ray diffraction, and beam bending viscometry

    Energy Technology Data Exchange (ETDEWEB)

    Ovono Ovono, D.; Berre, S.; Pradeau, P.; Comte, M. [Corning SAS, Corning European Technology Center, 7 bis, avenue de Valvins, 77210 Avon (France); Bruno, G., E-mail: brunog@corning.com [Corning SAS, Corning European Technology Center, 7 bis, avenue de Valvins, 77210 Avon (France)

    2012-01-10

    Highlights: Black-Right-Pointing-Pointer The crystallization of LAS glass was investigated using XRD, DSC and beam bending viscometry. Black-Right-Pointing-Pointer Different models were used to determine the kinetic parameters for crystallization. Black-Right-Pointing-Pointer The activation energy and Avrami parameters obtained are consistent with reported values. Black-Right-Pointing-Pointer The crystallization of LAS glass occurs with three-dimensional crystals growth. - Abstract: The crystallization kinetics of a commercial lithium-aluminum silicate (LAS) glass were characterized by differential scanning calorimetry (DSC) under non-isothermal conditions, by in-situ X-ray diffraction, and by three point beam bending viscosimeter (BBV). Non-isothermal DSC experiments were conducted at different heating rates. Results show that the crystal growth is controlled by a thermally activated process of the Arrhenius type. The activation energies obtained from isoconversional analysis are close to that extracted using the Johnson-Mehl-Avrami equation. While X-ray diffraction volume fraction data confirm the DSC analysis, it also shows that the crystallite size changes only at the end of the heat treatment protocol, during a hold at temperatures as high as 1000 Degree-Sign C. In this latter case, the crystal growth follows the Ostwald ripening mechanism. Finally, the viscosity measured in the crystallization region by BBV provides the activation energy for viscous flow, and it is slightly higher than the values obtained by DSC.

  20. Synthesis, X-ray crystal structures and catecholase activity investigation of new chalcone ligands

    Science.gov (United States)

    Thabti, Salima; Djedouani, Amel; Rahmouni, Samra; Touzani, Rachid; Bendaas, Abderrahmen; Mousser, Hénia; Mousser, Abdelhamid

    2015-12-01

    The reaction of dehydroacetic acid DHA carboxaldehyde and RCHO derivatives (R = quinoleine-8-; indole-3-; pyrrol-2- and 4-(dimethylamino)phenyl - afforded four new chalcone ligands (4-hydroxy-6-methyl-3-[(2E)-3-quinolin-8-ylprop-2-enoyl]-2H-pyran-2-one) L1, (4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one) L2, (4-hydroxy-6-methyl-3-[(2E)-3-(1H-pyrrol-2-yl)prop-2-enoyl]-2H-pyran-2-one) L3, and (3-{(2E)-3-[4-(dimethylamino)phenyl]prop-2-enoyl}-4-hydroxy-6-methyl-2H-pyran-2-one) L4. L3 and L4 were characterized by X-ray crystallography. Molecules crystallize with four and two molecules in the asymmetric unit, respectively and adopt an E conformation about the Cdbnd C bond. Both structures are stabilized by an extended network O-H … O. Furthermore, N-H … O and C-H … O hydrogen bonds are observed in L3 and L4 structures, respectively. The in situ generated copper (II) complexes of the four compounds L1, L2, L3 and L4 were examined for their catalytic activities and were found to catalyze the oxidation reaction of catechol to o-quinone under atmospheric dioxygen. The rates of this oxidation depend on three parameters: ligand, ion salts and solvent nature and the combination L2[Cu (CH3COO)2] leads to the faster catalytic process.

  1. Diffraction of X-ray free-electron laser femtosecond pulses on single crystals in the Bragg and Laue geometry.

    Science.gov (United States)

    Bushuev, V A

    2008-09-01

    A solution of the problem of dynamical diffraction for X-ray pulses with arbitrary dimensions in the Bragg and Laue cases in a crystal of any thickness and asymmetry coefficient of reflection is presented. Analysis of pulse form and duration transformation in the process of diffraction and propagation in a vacuum is conducted. It is shown that only the symmetrical Bragg case can be used to avoid smearing of reflected pulses.

  2. Experimental results from an X-ray imaging crystal spectrometer utilizing multi-wire proportional counter for KSTAR

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S. G., E-mail: sglee@nfri.re.kr; Kim, Y. S. [National Fusion Research Institute, Daejeon (Korea, Republic of); Yoo, J. W. [Korea University of Science and Technology, Daejeon (Korea, Republic of); Nam, U. W. [Korea Astronomy and Space Science Institute, Daejeon (Korea, Republic of); Moon, M. K. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-11-15

    The inconsistency of the first experimental results from the X-ray imaging crystal spectrometer for the Korea Superconducting Tokamak Advanced Research device utilizing a multi-wire proportional counter (MWPC) is clarified after improving the photon-count rate of the data acquisition system for the MWPC and ground loop isolator for the whole spectrometer system. The improved MWPC is successfully applied to pure Ohmic plasmas as well as plasmas with high confinement modes.

  3. Experimental results from an X-ray imaging crystal spectrometer utilizing multi-wire proportional counter for KSTAR

    Science.gov (United States)

    Lee, S. G.; Yoo, J. W.; Kim, Y. S.; Nam, U. W.; Moon, M. K.

    2016-11-01

    The inconsistency of the first experimental results from the X-ray imaging crystal spectrometer for the Korea Superconducting Tokamak Advanced Research device utilizing a multi-wire proportional counter (MWPC) is clarified after improving the photon-count rate of the data acquisition system for the MWPC and ground loop isolator for the whole spectrometer system. The improved MWPC is successfully applied to pure Ohmic plasmas as well as plasmas with high confinement modes.

  4. An X-ray microsource based system for crystal screening and beamline development during synchrotron shutdown periods

    Science.gov (United States)

    Miller, Mitchell D.; Deacon, Ashley M.

    2007-01-01

    Crystallographic end-stations require a significant investment in state-of-the-art equipment, as well as a significant effort in software development. The equipment often sits idle during annual maintenance shutdowns. In order to utilize the existing hardware and software during these shutdowns, we installed a sealed-tube microsource X-ray generator in the beamline 9-2 hutch at Stanford Synchrotron Radiation Laboratory. A multi-layer optic provides good flux and spectral purity. The small physical size of the source, the long optic to focus distance (635 mm) and the short source to optic distance (65 mm) allowed the use of existing beamline components, without any significant modification. The system replaces a short section of beam pipe upstream of the beam conditioning slits and shutter. The system can be installed and removed from the beamline in less than 1 day. The Joint Center for Structural Genomics (JCSG) and SSRL Structural Molecular Biology group developed the Stanford Automated Mounting (SAM) system and installed it on beamlines at SSRL. The JCSG relies on this system to test crystals for diffraction. The installation of the X-ray microsource in beamline 9-2 allowed crystal screening to continue during SSRL shutdowns. Using a standard screening protocol of two 10 minute exposures, separated by a 90° phi rotation, the system was capable of screening up to 400 crystals per week and was left to run unattended for up to 4 days. Over 8200 crystals were screened during the last four SSRL shutdown periods. An X-ray generator can also be useful for ongoing beamline development. Shutdown periods provide easier access to the experimental hardware, however, some tests require beam. The X-ray microsource offers the ability to conduct these tests during periods when users are not scheduled. PMID:19005562

  5. Development of an X-ray installation for the study of secondary electrons: preliminary measurements and calculations

    Energy Technology Data Exchange (ETDEWEB)

    Baguena, A.; Shaw, M.; Williart, A. [Universidad Nacional de Educacion a Distancia, Dpto. Fisica de los Materiales, Madrid (Spain); Baguena, A. [Consejo de Seguridad Nuclear, Madrid (Spain); Garcia, G. [Instituto de Matematicas y Fisica Fundamental, Consejo Superior de Investigaciones Cientificas, Madrid (Spain)

    2006-07-01

    We describe the calculations and preliminary measures made for the installation of a X-ray generator tube. This device is going to be used for the secondary electron production from photonic primary radiation of up to 125 keV. With this experimental system, we will study the energetic and space distribution of produced secondary electrons by obtaining its spectrum of energies and its angular distribution. This method of measurement is going to be applied in different targets of radiological, environmental and biological interest. Calculations in the present article include: theoretical yield of X-rays production of the designed equipment, necessary shielding for the radiological safety of the installation staff, and an estimated dose due to their use. Characteristics of the installation and the equipment are described with this purpose. (author)

  6. Gaseous electron multiplier-based soft x-ray plasma diagnostics development: Preliminary tests at ASDEX Upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Chernyshova, M., E-mail: maryna.chernyshova@ipplm.pl; Malinowski, K.; Czarski, T.; Kowalska-Strzęciwilk, E. [Institute of Plasma Physics and Laser Microfusion, Hery 23, 01-497 Warsaw (Poland); Wojeński, A.; Poźniak, K. T.; Kasprowicz, G.; Krawczyk, R.; Kolasiński, P.; Zabołotny, W.; Zienkiewicz, P. [Institute of Electronic Systems, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw (Poland); Vezinet, D.; Herrmann, A. [Max Planck Institute for Plasma Physics, Boltzmannstr. 2, 85748 Garching (Germany); Mazon, D.; Jardin, A. [CEA, IRFM, F-13108 Saint-Paul-lez-Durance (France)

    2016-11-15

    A Gaseous Electron Multiplier (GEM)-based detector is being developed for soft X-ray diagnostics on tokamaks. Its main goal is to facilitate transport studies of impurities like tungsten. Such studies are very relevant to ITER, where the excessive accumulation of impurities in the plasma core should be avoided. This contribution provides details of the preliminary tests at ASDEX Upgrade (AUG) with a focus on the most important aspects for detector operation in harsh radiation environment. It was shown that both spatially and spectrally resolved data could be collected, in a reasonable agreement with other AUG diagnostics. Contributions to the GEM signal include also hard X-rays, gammas, and neutrons. First simulations of the effect of high-energy photons have helped understanding these contributions.

  7. Bacterial expression, purification and preliminary X-ray crystallographic characterization of the invertase inhibitor Nt-CIF from tobacco.

    Science.gov (United States)

    Hothorn, Michael; Bonneau, Fabien; Stier, Gunter; Greiner, Steffen; Scheffzek, Klaus

    2003-12-01

    Acid invertases catalyzing the breakdown of sucrose are regulated at the post-translational level by extracellular inhibitory proteins of 16-20 kDa molecular weight in a pH-dependent manner. Little is known about the characteristics of the underlying protein-protein interaction. Here, the expression, purification, characterization, crystallization and initial X-ray analysis of a biologically active invertase inhibitor Nt-CIF from tobacco is reported. Four crystal forms covering a wide pH range have been obtained and data sets at resolutions higher than 2.5 A have been collected.

  8. Preliminary Research on Dual-Energy X-Ray Phase-Contrast Imaging

    CERN Document Server

    Han, Huajie; Gao, Kun; Wang, Zhili; Zhang, Can; Yang, Meng; Zhang, Kai; Zhu, Peiping

    2015-01-01

    Dual-energy X-ray absorptiometry (DEXA) has been widely applied to measure bone mineral density (BMD) and soft-tissue composition of human body. However, the use of DEXA is greatly limited for low-Z materials such as soft tissues due to their weak absorption. While X-ray phase-contrast imaging (XPCI) shows significantly improved contrast in comparison with the conventional standard absorption-based X-ray imaging for soft tissues. In this paper, we propose a novel X-ray phase-contrast method to measure the area density of low-Z materials, including a single-energy method and a dual-energy method. The single-energy method is for the area density calculation of one low-Z material, while the dual-energy method is aiming to calculate the area densities of two low-Z materials simultaneously. Comparing the experimental and simulation results with the theoretic ones, the new method proves to have the potential to replace DEXA in area density measurement. The new method sets the prerequisites for future precise and lo...

  9. Cs2AgBiBr6 single-crystal X-ray detectors with a low detection limit

    Science.gov (United States)

    Pan, Weicheng; Wu, Haodi; Luo, Jiajun; Deng, Zhenzhou; Ge, Cong; Chen, Chao; Jiang, Xiaowei; Yin, Wan-Jian; Niu, Guangda; Zhu, Lujun; Yin, Lixiao; Zhou, Ying; Xie, Qingguo; Ke, Xiaoxing; Sui, Manling; Tang, Jiang

    2017-11-01

    Sensitive X-ray detection is crucial for medical diagnosis, industrial inspection and scientific research. The recently described hybrid lead halide perovskites have demonstrated low-cost fabrication and outstanding performance for direct X-ray detection, but they all contain toxic Pb in a soluble form. Here, we report sensitive X-ray detectors using solution-processed double perovskite Cs2AgBiBr6 single crystals. Through thermal annealing and surface treatment, we largely eliminate Ag+/Bi3+ disordering and improve the crystal resistivity, resulting in a detector with a minimum detectable dose rate as low as 59.7 nGyair s-1, comparable to the latest record of 0.036 μGyair s-1 using CH3NH3PbBr3 single crystals. Suppressed ion migration in Cs2AgBiBr6 permits relatively large external bias, guaranteeing efficient charge collection without a substantial increase in noise current and thus enabling the low detection limit.

  10. The Catalytic Conversion of Thiophenes over Large H-ZSM-5 Crystals: An X-Ray, UV/Vis, and Fluorescence Microspectroscopic Study

    NARCIS (Netherlands)

    Kox, M.H.F.; Mijovilovich, A.E.; S ättler, J.J.H.B.; Stavitski, I.; Weckhuysen, B.M.

    2013-01-01

    X-ray absorption, UV/Vis, and fluorescence microspectroscopy have been used to characterize the catalytic conversion of thiophene derivatives within the micropores of an individual H-ZSM-5 zeolite crystal. Space-resolved information into the Si/ Al ratios and sulfur content was provided by X-ray

  11. Disputed discovery: the beginnings of X-ray diffraction in crystals in 1912 and its repercussions.

    Science.gov (United States)

    Eckert, Michael

    2012-01-01

    The discovery of X-ray diffraction is reviewed from the perspective of the contemporary knowledge in 1912 about the nature of X-rays. Laue's inspiration that led to the experiments by Friedrich and Knipping in Sommerfeld's institute was based on erroneous expectations. The ensuing discoveries of the Braggs clarified the phenomenon (although they, too, emerged from dubious assumptions about the nature of X-rays). The early misapprehensions had no impact on the Nobel Prizes to Laue in 1914 and the Braggs in 1915; but when the prizes were finally awarded after the war, the circumstances of `Laue's discovery' gave rise to repercussions. Many years later, they resulted in a dispute about the `myths of origins' of the community of crystallographers.

  12. Crystal chemistry, surface morphology and X-ray photoelectron spectroscopy of Fe-rich osumilite from Mt. Arci, Sardinia (Italy)

    Science.gov (United States)

    Elmi, Chiara; Brigatti, Maria Franca; Pasquali, Luca; Montecchi, Monica; Laurora, Angela; Malferrari, Daniele; Nannarone, Stefano

    2010-09-01

    Microprobe analysis, single crystal X-ray diffraction, X-ray photoelectron spectroscopy, atomic force microscopy, and X-ray absorption spectroscopy were applied on Fe-rich osumilite from the volcanic massif of Mt. Arci, Sardinia, Italy. Osumilite belongs to the space group P6/ mcc with unit cell parameters a = 10.1550(6), c = 14.306(1) Å and chemical formula (K0.729)C (Na0.029)B (Si10.498 Al1.502)T1 (Al2.706 Fe{0.294/2+})T2 (Mg0.735 Mn0.091 Fe{1.184/2+})AO30. Structure refinement converged at R = 0.0201. Unit cell parameter a is related to octahedral edge length as well as to Fe2+ content, unlike the c parameter which does not seem to be affected by chemical composition. The determination of the amount of each element on the mineral surface, obtained through X-ray photoelectron spectroscopy high-resolution spectra in the region of the Si2p, Al2p, Mg1s and Fe2p core levels, suggests that Fe presents Fe2+ oxidation state and octahedral coordination. Two peaks at 103.1 and 100.6 eV can be related to Si4+ and Si1+ components, respectively, both in tetrahedral coordination. The binding energy of Al2p, at 74.5 eV, indicates that Al is mostly present in the distorted T2 site, whereas the Mg peak at 1,305.2 eV suggests that this cation is located at the octahedral site. X-ray absorption at the Fe L2,3-edges confirms that iron is present in the mineral structure, prevalently in the divalent state and at the A octahedral site.

  13. Synthesis, characterization and single crystal X-ray analysis of chlorobis(N,N-dimethyldithiocarbamato-S,S′)antimony(III)

    OpenAIRE

    Chauhan, H.P.S.; Jaswant Carpenter

    2015-01-01

    The title compound chlorobis(N,N-dimethyldithiocarbamato-S,S′)antimony(III) has been prepared in distilled acetonitrile and characterized by physicochemical [melting point and molecular weight determination, elemental analysis (C, H, N, S & Sb)], spectral [FT–IR, far IR, NMR (1H & 13C)] studies. The crystal and molecular structure was further confirmed using single crystal X-ray diffraction analysis which features a five-coordinate geometry for antimony(III) within a ClS4 donor set. The disto...

  14. Strength of shock-loaded single-crystal tantalum [100] determined using in situ broadband x-ray Laue diffraction.

    Science.gov (United States)

    Comley, A J; Maddox, B R; Rudd, R E; Prisbrey, S T; Hawreliak, J A; Orlikowski, D A; Peterson, S C; Satcher, J H; Elsholz, A J; Park, H-S; Remington, B A; Bazin, N; Foster, J M; Graham, P; Park, N; Rosen, P A; Rothman, S R; Higginbotham, A; Suggit, M; Wark, J S

    2013-03-15

    The strength of shock-loaded single crystal tantalum [100] has been experimentally determined using in situ broadband x-ray Laue diffraction to measure the strain state of the compressed crystal, and elastic constants calculated from first principles. The inferred strength reaches 35 GPa at a shock pressure of 181 GPa and is in excellent agreement with a multiscale strength model [N. R. Barton et al., J. Appl. Phys. 109, 073501 (2011)], which employs a hierarchy of simulation methods over a range of length scales to calculate strength from first principles.

  15. Plastic deformation of copper single crystals by simulation using X-ray Lang method and molecular dynamics

    CERN Document Server

    Doyama, M; Nozaki, T; Kato, Y

    2003-01-01

    Copper rectangular parallelepiped single crystals with a notch have been extended or compressed. In a crystal with a notch, partial dislocations were created near the tip of the notch in elongation as we expected. It is hard to see where the dislocations were created just looking the displaced positions of atoms, but by a simulation of X-ray Lang topography, the creation of dislocations was easily observed. Before creation of dislocations, some indication was quite clearly shown. For compression dislocations did not start near the tip of the notch but started uniformly on the surface, the effect of notch was minor.

  16. Interactions between X-ray induced transient defects and pre-existing damage precursors in DKDP crystals

    Energy Technology Data Exchange (ETDEWEB)

    Negres, R A; Saw, C K; Demos, S G

    2008-10-24

    Large-aperture laser systems, currently designed to achieve high energy densities at the target location (exceeding {approx} 10{sup 11} J/m{sup 3}), will enable studies of the physics of matter and radiation under extreme conditions. As a result, their optical components, such as the frequency conversion crystals (KDP/DKDP), may be exposed to X-rays and other ionizing radiation. This in turn may lead to a change in the damage performance of these materials as they may be affected by radiation-induced effects by either forming new damage initiation centers or interacting with the pre-existing damage initiating defects (so-called damage precursors). We present an experimental study on the laser-induced bulk damage performance at 355-nm of DKDP crystals following X-ray irradiation at room temperature. Results indicate that the damage performance of the material is affected by exposure to X-rays. We attribute this behavior to a change in the physical properties of the precursors which, in turn, affect their individual damage threshold.

  17. High-sensitivity, portable, tunable imaging X-ray spectrometer based on a spherical crystal and MCP

    CERN Document Server

    Monot, P; Dobosz, S; D'Oliveira, P; Hulin, S; Bougeard, M; Faenov, A Y; Pikuz, T A; Skobelev, I Y

    2002-01-01

    A portable (200x100x100 mm sup 3), high-luminosity, spherically bent crystal spectrometer was designed to measure very low emissivity X-ray spectra of different elements with spatial resolution in a wide spectral range (1.2-19.6 A). A large (50x15 mm sup 2) open aperture mica spherically bent crystal with R=150 mm was used as dispersive and focusing element. This spectrometer was associated with a large sensitive area (phi=40 mm) micro-channel plates assembly. This apparatus provides simultaneously high spectral (lambda/delta lambda approx 1800) and spatial (100-200 mu m) resolutions. Its large tunability allowed, without any adjustment of the spectrometer set-up, to record spectra in the 1.38-17.5 A wavelength range. We used the X-ray emission of femtosecond laser-produced plasmas from different materials ((CF sub 2) sub n , CaF sub 2 , Cu, Al) to test the spectrometer. Thanks to the high sensitivity (high collection efficiency) of the system, high quality space-resolved X-ray spectra of Fluorine and Aluminu...

  18. Monolithic integration of hybrid perovskite single crystals with heterogenous substrate for highly sensitive X-ray imaging

    Science.gov (United States)

    Wei, Wei; Zhang, Yang; Xu, Qiang; Wei, Haotong; Fang, Yanjun; Wang, Qi; Deng, Yehao; Li, Tao; Gruverman, Alexei; Cao, Lei; Huang, Jinsong

    2017-04-01

    The monolithic integration of new optoelectronic materials with well-established inexpensive silicon circuitry is leading to new applications, functionality and simple readouts. Here, we show that single crystals of hybrid perovskites can be integrated onto virtually any substrates, including silicon wafers, through facile, low-temperature, solution-processed molecular bonding. The brominated (3-aminopropyl)triethoxysilane molecule binds the native oxide of silicon and participates in the perovskite crystal with its ammonium bromide group, yielding a solid mechanical and electrical connection. The dipole of the bonding molecule reduces device noise while retaining signal intensity. The reduction of dark current enables the detectors to be operated at increased bias, resulting in a sensitivity of 2.1 × 104 µC Gyair-1 cm-2 under 8 keV X-ray radiation, which is over a thousand times higher than the sensitivity of amorphous selenium detectors. X-ray imaging with both perovskite pixel detectors and linear array detectors reduces the total dose by 15-120-fold compared with state-of-the-art X-ray imaging systems.

  19. Preliminary research on organics recognition by x-ray absorption spectroscopy detection and classification

    Science.gov (United States)

    Wang, Qian; Wu, Xiaomei; Zhang, Wei; He, Shuting; Feng, Haifeng; Fang, Zheng

    2016-01-01

    X-ray Absorption Spectroscopy (XAS) was been applied for the material recognition in this paper. Twelve kinds of plastics were selected as specimens. Each specimen was tested for 100 times by different operators for data processing. Seventy sets of spectral data of each specimen were randomly selected as training set and the other 30 sets were selected as testing set. Training set was calculated with Principal Component Analysis (PCA) to get the first four Principal Components, which totally explain 99% of the original spectrum. The first four Principal Components were built plastic classification model respectively through K-Nearest Neighbor (KNN) and Support Vector Machine (SVM) methods. The classification accuracy reached 89.22%-98.17%. Experimental results demonstrate that organics could be recognized by XAS. It shows that the X-ray absorption spectroscopy contains the potential of other organics recognition or even organisms.

  20. Quasi-mosaic Crystals For High-resolution Focusing Of Hard X-rays Through A Laue Lens

    Science.gov (United States)

    Camattari, R.; Guidi, V.; Bellucci, V.; Neri, I.

    2011-09-01

    We propose the usage of bent crystals exploiting the Quasi-Mosaicity for high-resolution focusing of hard X-rays. Quasi-Mosaicity is an effect of anisotropy in crystals that manifests itself along selected crystallographic directions. As a result of primary curvature imparted to the crystal, a secondary curvature (Quasi-Mosaic curvature) occurs. We demonstrated that a combination of primary and Quasi-Mosaic curvatures allows high-efficiency diffraction and high-resolution focusing of diffracted photons. As compared to traditional mosaic crystals with same size and energy passband, Quasi-Mosaic crystals would increases the signal-to-noise ratio by about an order of magnitude and no mosaic defocusing would occur.

  1. Symmetry Aspects of Dislocation-Effected Crystal Properties: Material Strength Levels and X-ray Topographic Imaging

    Directory of Open Access Journals (Sweden)

    Ronald W. Armstrong

    2014-03-01

    Full Text Available Several materials science type research topics are described in which advantageous use of crystal symmetry considerations has been helpful in ferreting the essential elements of dislocation behavior in determining material properties or for characterizing crystal/polycrystalline structural relationships; for example: (1 the mechanical strengthening produced by a symmetrical bicrystal grain boundary; (2 cleavage crack formation at the intersection within a crystal of symmetrical dislocation pile-ups; (3 symmetry aspects of anisotropic crystal indentation hardness measurements; (4 X-ray diffraction topography imaging of dislocation strains and subgrain boundary misorientations; and (5 point and space group aspects of twinning. Several applications are described in relation to the strengthening of grain boundaries in nanopolycrystals and of multiply-oriented crystal grains in polysilicon photovoltaic solar cell materials. A number of crystallographic aspects of the different topics are illustrated with a stereographic method of presentation.

  2. High-pressure X-ray diffraction of L-ALANINE crystal

    DEFF Research Database (Denmark)

    Olsen, J.S.; Gerward, Leif; Souza, A.G.

    2006-01-01

    L-ALANINE has been studied by X-ray diffraction at ambient temperature and pressure up to 10.3 GPa. The material is found to transform to a tetragonal structure between 2 and 3 GPa. and to a monoclinic structure between 8 and 10 GPa. The experimental bulk modulus is 25(5) GPa for the orthorhombic...

  3. Investigation of early growth of calcium hydroxide crystals in cement solution by soft x-ray transmission microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Harutyunyan, V. S.; Kirchheim, A. P.; Monteiro, P. J. M.; Aivazyan, A. P.; Fischer, P.

    2009-02-02

    Research on cement hydration was performed at the full-field soft transmission X-ray microscope XM-1 located at beamline 6.1.2 at the Advanced Light Source (ALS) in Berkeley CA which is operated by the Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, California. A series of works [1-3] has been conducted using this microscope for the in situ observation and qualitative analysis of through-solution hydration products and products of topochemical reactions, which form in cementitious aqueous solutions. This paper studies the precipitation of the calcium hydroxide (CH) crystals from the cement solution. The analysis of successive images of the hydration process provides critical quantitative information about the growth rate of calcium hydroxide (CH) crystals, the supersaturation ratio, and the kinetic and diffusion coefficients of the growth process. ASTM Type II portland cement and 6% C{sub 4}A{sub 3}{bar S} admixture were mixed in aqueous solution and saturated with respect to CH and gypsum. The C{sub 4}A{sub 3}{bar S} admixture was included in the experimental program because of the general research program on expansive cements, and adding C{sub 4}A{sub 3}{bar S} to portland cement is an efficient method of generating ettringite and significant early-age expansion. The solution/solid materials ratio was 10 cm{sup 3}/g, which is higher than the one existing in regular concrete and mortars; to compensate for this dilution, the solution was originally saturated with CH and gypsum. To allow sufficient transmission of the soft X-rays, a small droplet was taken from the supernatant solution and assembled in the sample holder, and then squeezed between two silicon nitride windows for the analysis. The X-ray optical setup of the microscope XM-1 is described elsewhere [2]. In this experiment, a wavelength of 2.4 nm (516.6 eV) was used. The radiation transmitting the sample was detected using an X-ray CCD camera, with a resolution of 35 nm provided

  4. Quantitative energy-dispersive x-ray diffraction for identification of counterfeit medicines: a preliminary study

    Science.gov (United States)

    Crews, Chiaki C. E.; O'Flynn, Daniel; Sidebottom, Aiden; Speller, Robert D.

    2015-06-01

    The prevalence of counterfeit and substandard medicines has been growing rapidly over the past decade, and fast, nondestructive techniques for their detection are urgently needed to counter this trend. In this study, energy-dispersive X-ray diffraction (EDXRD) combined with chemometrics was assessed for its effectiveness in quantitative analysis of compressed powder mixtures. Although EDXRD produces lower-resolution diffraction patterns than angular-dispersive X-ray diffraction (ADXR