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

蛋白质分子替代全自动软件系统MrPDB的开发

• 批准号: 12480181
• 负责人: KUSUNOKI Masami
• 金额: $ 4.61万
• 依托单位: Osaka University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2000
• 资助国家: 日本
• 起止时间: 2000 至 2002
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-12480181/
• 关键词: Molecular replacement; Protein Data Bank; Protein; crystal; X-ray; software; 自動解析

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.

蛋白质的晶体结构可以通过X射线晶体学来确定。蛋白质的晶体结构已被保存在蛋白质数据库中。如果序列同一性大于30%的同源蛋白质的晶体结构已经在蛋白质数据库中，则可以通过分子置换方法确定蛋白质的晶体结构，其中仅需要晶体的天然结构因子数据，因此结构确定的过程是直接的。我们开发了Mr-PDB，基于WEB的蛋白质结构测定分子置换自动化软件系统。用户在MrPDB的WEB页面中输入晶体数据、氨基酸序列，并将晶体结构因子文件上传到MrPDB的WEB服务器。然后MrMDP自动确定蛋白质的晶体结构。

项目成果

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)

T.Tanikawa、M.Kusunoko、T.Fukmi：“UDR 葡萄糖原磷酸化酶：一级结构和亲和力标记”生物化学、分子生物学和生物物理学杂志。

Miyake その他: "Analysis of Catalytic Mechanism of β-amylase from Bacillus cereus"Biochemistry. 42. 5574-5581 (2003)

Miyake等人：“蜡状芽孢杆菌β-淀粉酶的催化机制分析”生物化学42. 5574-5581(2003)。

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)

Masami Kusunoki：“获得蛋白质、核酸和酶的 3D 结构”，第 96 卷，第 13 期（2001 年）。

Yamamoto その他: "Crystal Structure of Glucose Dehydrogenase from Bacillus"Journal of Biochemistry. 129. 303-312 (2001)

Yamamoto 等：“来自芽孢杆菌的葡萄糖脱氢酶的晶体结构”生物化学杂志 129. 303-312 (2001)。

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. V

Miyake, H.、Kurisu, G.、Kusunoki, M.、Nishimura, S. 和 Nitta, Y.：“通过催化的 X 射线晶体结构分析蜡状芽孢杆菌蕈状芽孢杆菌 β-淀粉酶的催化机制与麦芽五糖共结晶的残留突变体”生物化学。V