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Yorodumi- PDB-2ayq: 3-ISOPROPYLMALATE DEHYDROGENASE FROM THE MODERATE FACULTATIVE THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ayq | |||||||||
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Title | 3-ISOPROPYLMALATE DEHYDROGENASE FROM THE MODERATE FACULTATIVE THERMOPHILE, BACILLUS COAGULANS | |||||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / 3-ISOPROPYLMALATE DEHYDROGENASE / LEUCINE BIOSYNTHESIS / MODERATE THERMOPHILE | |||||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus coagulans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Tsuchiya, D. / Takenaka, A. | |||||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1997 Title: Crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile, Bacillus coagulans: two strategies for thermostabilization of protein structures. Authors: Tsuchiya, D. / Sekiguchi, T. / Takenaka, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of 3-Isopropylmalate Dehydrogenase from the Moderate Facultative Thermophile Bacillus Coagulans Authors: Tsuchiya, D. / Matsumoto, O. / Gorai, T. / Sekiguchi, T. / Nosoh, Y. / Takenaka, A. #2: Journal: Biochim.Biophys.Acta / Year: 1986 Title: DNA and Amino-Acid Sequences of 3-Isopropylmalate Dehydrogenase of Bacillus Coagulans. Comparison with the Enzymes of Saccharomyces Cerevisiae and Thermus Thermophilus Authors: Sekiguchi, T. / Ortega-Cesena, J. / Nosoh, Y. / Ohashi, S. / Tsuda, K. / Kanaya, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ayq.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ayq.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ayq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/2ayq ftp://data.pdbj.org/pub/pdb/validation_reports/ay/2ayq | HTTPS FTP |
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-Related structure data
Related structure data | 1ipdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.261146, -0.367011, -0.892808), Vector: |
-Components
#1: Protein | Mass: 39855.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus coagulans (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P12010, 3-isopropylmalate dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD. | ||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 6 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. obs: 25540 / % possible obs: 84.5 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 3→3.18 Å / % possible all: 62.6 |
Reflection | *PLUS Num. measured all: 101970 |
Reflection shell | *PLUS % possible obs: 62.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IPD Resolution: 3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 3
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.13 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.266 |