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Development of MrPDB, a full automatic software system of molecular replacement for protein

Research Project

Project/Area Number 12480181
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionOsaka University

Principal Investigator

KUSUNOKI Masami  Osaka University, Institute for Protein Research, Associate Professor, たんぱく質研究所, 助教授 (90135749)

Co-Investigator(Kenkyū-buntansha) TANAKA Nobuo  Tokyo Institute of Technology, Graduate School of Bioscience and Bitechnology, professor, 大学院・生命理工学研究科, 教授 (50032024)
KURISU Genji  Osaka University, Institute for Protein Research, Research Associate, たんぱく質研究所, 助手 (90294131)
Project Period (FY) 2000 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥7,200,000 (Direct Cost: ¥7,200,000)
Fiscal Year 2002: ¥2,100,000 (Direct Cost: ¥2,100,000)
Fiscal Year 2001: ¥2,100,000 (Direct Cost: ¥2,100,000)
Fiscal Year 2000: ¥3,000,000 (Direct Cost: ¥3,000,000)
KeywordsMolecular replacement / Protein Data Bank / Protein / crystal / X-ray / software / 自動解析
Research Abstract

Crystal structure of a protein can be determined by X-ray crystallography. Solved crystal structures of proteins have been deposited in the Protein Data Bank. If a crystal structure of a homologous protein with sequence identity greater than 30 % is already in the Protein Data Bank, then the crystal structure of the protein can be determined by the molecular replacement method, in which only native structure factor data of crystals are needed and hence the process of structure determination is straightforward.
We have developed Mr-PDB, a WEB-based automatic software system of molecular replacement for protein structure determination. The user input crystal data, amino-acid sequence in the WEB page of MrPDB and upload the file of crystal structure factors to the WEB server of MrPDB. Then MrMDP determines the crystalstructure of the protein automatically.

Report

(4 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (15 results)

All Other

All Publications (15 results)

  • [Publications] Kurisu, Kusunoki その他: "Structure of the Electron Transfer Complex between Ferredoxin"Nature Structural Biology. 8. 117-121 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yamamoto その他: "Crystal Structure of Glucose Dehydrogenase from Bacillus"Journal of Biochemistry. 129. 303-312 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Otagiri その他: "Crystal Structure of meso-2, 3-Butanediol Dehydrogenase in Complex"Journal of Biochemistry. 129. 205-208 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Miyake その他: "Analysis of Catalytic Mechanism of β-amylase from Bacillus cereus"Biochemistry. 42. 5574-5581 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kurisu, G., Kusunoki, M., Katoh, E., Yamazaki, T., Teshima, K., Onda, Y., Kimata-Ariga, Y., and Hase, T.: "Structure of the Electron Transfer Complex between Ferredoxin and Ferredoxin-NADP^+ Reductase"Nature Structural Biology. Vol.8, No.2. 117-121 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yamamoto, K., Kurisu, G., Kusunoki, M., Tabata, S., Urabe, I., and S. Osaki, S.: "Crystal Structure of Glucose Dehydrogenase from Bacillus megaterium IWG3 at 1.7 A Resolution"Journal of Biochemistry. Vol.129, No.2. 303-312 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Otagiri, M., Kurisu, G., Ui, S., Takusagawa, Y., Ohkuma, M., Kudo, T. and Kusunoki, M.: "Crystal Structure of meso-2, 3-Butanediol Dehydrogenase in Complex with Inhibitor Mercaptoethanol at 1.7 A Resolution for Undertanding of Chiral Recognition Mechanismsfroms"Journal of Biochemistry. Vol.129, No.2. 205-208 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Miyake, H., Kurisu, G., Kusunoki, M., Nishimura, S., and Nitta, Y.: "Analysis of Catalytic Mechanism of β-amylase from Bacillus cereus var. mycoides by X-ray Crystal Structure of a Catalytic Residue Mutant Cocrystallized with Maltopentaose"Biochemistry. Vol.42. 5574-5581 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Hatakeyama, T., Kusunoki, M.その他: "Crystallization and Preliminary Crystallographic Study of an Invertebrate C-type Lectin, CEL-I, from a Marine Invertebrate Cucumaria echinata"Acta Crystallographica. Vol.D51 No.1. 143-144 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Katakawa, K., Kusunoki, M.その他: "Crystal and Molecular Structure of a New Diterpenyl Glycoside from Preris cretics L"Journal of Chemical Crystallography. Vol.32 No.1-2. 39-42 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] G.Kurisu, M.Kusunoki 他6名: "Structure of the Electron Transfer Complex between Ferredoxin and Ferredoxin-NADP^+ Reductase"Nature Structural Biology. Vol.8,NO.2. 117-121 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 楠木 正巳: "立体構造を手に入れる"蛋白質・核酸・酵素. Vol.96,NO.13. 2003-2008 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.Tanigawa, M.Kusunoko, T.Fukmi: "UDR Glucose Prophosphorylase : Primary Structure and Affinity Labeling"Journal of Biochemical, Molecular Biology and Biophysics. Vol.5. 83-98 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] K.Yamamoto,M.Kasanoki 他3名: "Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterlum IWG 3"Acta Crystallographica. D56. 1443-1445 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] M.Otagiri,G.Karisn,S.Ui M.ikusncnoki: "Crystal Strcture of meso-2,3-butanediol dehydrogenate in a complex with NAD and inhibitor mercaptoethanol"Journal of Biochemisty . 129. 205-208 (2001)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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