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A Crystallographic Workbench and Its Use in Structure Analysis of Hydrogenase

Research Project

Project/Area Number 04403026
Research Category

Grant-in-Aid for General Scientific Research (A)

Allocation TypeSingle-year Grants
Research Field 結晶学
Research InstitutionHimeji Institute of Thchnology

Principal Investigator

YASUOKA Noritake  Faculty of Science, Himeji Institute of Thchnology, Professor10, 理学部, 教授 (40029054)

Co-Investigator(Kenkyū-buntansha) MISAKI Shintaro  Faculty of Science, Himeji Institute of Thchnology, Assistant, 理学部, 助手 (30244685)
HIGUCHI Yoshiki  Faculty of Science, Himeji Institute of Thchnology, Associate Professor, 理学部, 助教授 (90183574)
Project Period (FY) 1992 – 1994
Project Status Completed (Fiscal Year 1994)
Budget Amount *help
¥20,300,000 (Direct Cost: ¥20,300,000)
Fiscal Year 1994: ¥2,400,000 (Direct Cost: ¥2,400,000)
Fiscal Year 1993: ¥7,800,000 (Direct Cost: ¥7,800,000)
Fiscal Year 1992: ¥10,100,000 (Direct Cost: ¥10,100,000)
Keywordscrystallographic workbench / hydrogenase / X-ray analysis / anomalous scattering / isomorphous relacement / electron density / iron sulfur cluster / network / 鉄イオンクラスター / 鉄・イオウクラスター
Research Abstract

A crystallographic workbench or a crystallographic workstation installed with software packages and database systems is developed, which enables a through processing from X-ray measurement to protein structure analysis. As workstations have become more popular in many crystallography laboratories, a through X-ray analysis system is now able to be constructed via local area network. X-ray diffraction measurement apparatuses, Rigaku fourcircle single crystal diffractometer and MAC Science Image The construction of an integrated system of measuring the X-ray intensities from any crystal specimen, transferring structure factor data via network, carrying out the structure analysis and displaying the molecular structure.
The active centers of NiFe hydrogenase from Desulfovibrio vulgaris Miyazaki F has been located in the electron density map calculated at 4 * resolution. The electron density map based on five heavy atom derivatives showed four strong peaks which were clearly distinguished from the protein region. These strong densities have been successfully assigned to three iron-sulfur clusters and one nickel atom by difference Fourier technique with coefficients of the best phases from multiple isomorphous replacement (MIR) method and structure factors obtained at five wavelengths (1.040,1.487,1.730,1.743, and 1.750* with use of the synchrotron radiation source. Four active centers are approximately lined up with a distance of ca. 13* which seems to be reasonable for them to be connected with electron transfer chain.

Report

(4 results)
  • 1994 Annual Research Report   Final Research Report Summary
  • 1993 Annual Research Report
  • 1992 Annual Research Report
  • Research Products

    (27 results)

All Other

All Publications (27 results)

  • [Publications] Y.Higuchi,H.Akutsu and N.Yasuoka: "A detailed comparison of the refined structures of cytochrome c3 molecules from two strains in Desulfovibrio vulgaris:The relationship between the heme structures and redox properties" Biochimie. 76. 537-545 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] Y.Higuchi,S.Misaki,Y.Morimoto and N.Yasuoka: "Location of Active Sites of NiFe Hydrogenase determined by the Combination of Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods" Acta Crystallographica. D50. 781-785 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] I.Fujii,N.Hirayama,S.Misaki,Y.Higuchi and N.Yasuoka: "An Integrated X-ray Measurement and Computation System in Protein Crystallography Y.Higuchi," Bioimages. 2. 143-148 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] I.Fujii,N.Hirayama,Y.Higuchi,and N.Yasuoka: "XVIEWER-An Interactive Image Processing Program for Diffraction Data from the Weissenberg Camera for Macromolecular Crystallography" Bioimages. 2. 47-52 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] N.Yasuoka,S.Sugiyama,Y.Morimoto,Y.Higuchi: "On the Active Sites of Hydrogenase from Desulfovibrio vulgaris Miyazaki F" Jpn.J.Appl.Phys.32. 553-555 (1993)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] A.Yoneda,T.Hakushi,Y.Morimoto and N.Yasuoka: "Intramolecular Hydrogen Bonding Within Cyclometalated Palladium(II)Complex Containing L(-)-1-Phenylethylamine Ligand" Chemistry Letters. 175-176 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] Y.Higuchi, H.Akutsu, and N.Yasuoka: "A detailed comparison of the refined structures of cytochrome c3 molecules from two strains in Desulfovibrio vulgaris : The relationship between the heme structures and redox properties" Biochimie. 76. 537-545 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] Y.Higuchi, S.Misaki, Y.Morimoto and N.Yasuoka: "Location of Active Sites of NiFe Hydrogenase determined by the Combination of Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods" Acta Crystallographica. D50. 781-785 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] I.Fujii, N.Hirayama, S.Misaki, Y.Higuchi and N.Yasuoka: "An Integrated X-ray Measurement and Computation System in Proten Crystallography Y.Higuchi" Bioimages. 2. 143-148 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] I.Fujii, N.Hirayama, Y.Higuchi, and N.Yasuoka: "XVIEWER-An Interactive Image Processing Program for Diffraction Data from the Weissenberg Camera for Macromolecular Crystallography" Bioimages. 2. 47-52 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] N.Yasuoka, S.Sugiyama, Y.Morimoto.Y.Higuchi: "On the Active Sites of Hydrogenase from Desulfovibrio vulgaris Miyazaki F" Jpn.J.Appl.Phys.32. 553-555 (1993)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] A.Yoneda, To.Hakushi, Y.Morimoto and N.Yasuoka: "Intramolecular Hydrogen Bonding within Cyclometalated Palladium (II) Complex Containing L (-) -1-Phenylethylamine Ligand" Chemistry Letters. 175-176 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1994 Final Research Report Summary
  • [Publications] Y.Higuchi,H.Akutsu,and N.Yasuoka: "A detailed comparison of the refined structures of cytochrome c3 molecules from two strains in Desulfovibrio vulgaris:The relationship between the heme structures and redox properties" Biochimie. 76. 537-545 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Y.Higuchi,S.Misaki,Y.Morimoto and N.Yasuoka: "Location of Active Sites of NiFe Hydrogenase determined by the Combination of Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods" Acta Crystallographica. D50. 781-785 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] I.Fujii,N.Hirayama,S.Misaki,Higuchi,and N.Yasuoka: "An Integrated X‐ray Measurement and Computation System in Protein Crystallography Y." Bioimages. 2. 143-148 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] I.Fujii,N.Hirayama,Y.Higuchi,and N.Yasuoka: "XVIEWER‐An Interactive Image Processing Program for Diffraction Data from the Weissenberg Camera for Macromolecular Crystallography" Bioimages. 2. 47-52 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] N.Yasuoka,S.Sugiyama,Y.Morimote,Y.Higuchi: "On the Active Sites of Hydrogenase from Desulfovibrio vulgaris Miyazaki F" Jpn.J.Appl.Phys.32. 553-555 (1993)

    • Related Report
      1994 Annual Research Report
  • [Publications] A.Yoneda,T.Hakushi,Y.Morimoto and N.Yasuoka.: "Intramolecular Hydrogen Bonding within Cyclometalated Palladium(II) Complex Containing L(-)1-Phony lethy Iamine Ligand" Chemistry Letters. 175-176 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Y.Higuchi,S.Masaki, Y.Morimoto and N.Yasuoka: "Location of Active Sites of NiFe Hydrogenase determined by the Combination of Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods" Acta Crystallographica. D50(in the press). (1994)

    • Related Report
      1993 Annual Research Report
  • [Publications] I.Fujii,N.Hirayama, Y.Higuchi,and N.Yasuoka: "XVIEWER-An Interactive Image Processing Program for Diffraction Data from the Weissenberg Camera for Macromolecular Crystallography" Bioimages. 2. 47-52 (1994)

    • Related Report
      1993 Annual Research Report
  • [Publications] N.Yasuoka,S.Sugiyama, Y.Morimoto,Y.Higuchi: "On the Active Sites of Hydrogenase from Desulfovibrio vulgris Miyazaki F" Jpn.J.Appl.phys.32. 553-555 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] A.Yoneda,T.Hakushi, Y.Morimoto and N.Yasuoka: "Intramolecular Hydrogen Bonding within Cyclometalated Palladium(II) Complex Containing L(-)-1-Phenylethylamine Ligand" Chemistry Letters. 175-176 (1994)

    • Related Report
      1993 Annual Research Report
  • [Publications] 安岡則武: "放射光を用いた生体分子の構造研究" 放射線医学物理. 13. 186-194 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] 安岡則武: "タンパク質結晶構造解析法の進歩と問題点" 細胞工学. 12. 762-766 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] I.Fujii,Y.Morimoto,Y.Higuchi,N.Yasuoka: "XELE-a polypeptide model-building program for a workstation." J,Molecular Graphics. 10. 185-189 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] 中川 敦史,安岡 則武: "タンパク質の結晶構造解析計算のベンチワークテスト" 日本結晶学会誌. 34. 201-206 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] Y.Yoneda,G.R.newKome,N.Yasuoka: "Structures of Diethyl 2-[(Hydroxy k0-2quinolyl-quinolyl-kN)methyl malonato(2-)kC](pyridine)" Acta Cryst.C49. (1993)

    • Related Report
      1992 Annual Research Report

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Published: 1992-04-01   Modified: 2016-04-21  

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