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Yorodumi- PDB-1cnz: 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) FROM SALMONELLA TYPHIMURIUM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cnz | ||||||
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Title | 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) FROM SALMONELLA TYPHIMURIUM | ||||||
Components | PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / LEUCINE BIOSYNTHETIC PATHWAY / NAD-DEPENDANT ENZYME | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Wallon, G. / Kryger, G. / Lovett, S.T. / Oshima, T. / Ringe, D. / Petsko, G.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal Structures of Eschericia Coli and Salmonella Typhimurium 3- Isopropylmalate Dehydrogenase and Comparison with Their Thermophilic Counterpart from Thermus Thermophilus Authors: Wallon, G. / Kryger, G. / Lovett, S.T. / Oshima, T. / Ringe, D. / Petsko, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cnz.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cnz.ent.gz | 128.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/1cnz ftp://data.pdbj.org/pub/pdb/validation_reports/cn/1cnz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39556.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: LEU B / Production host: Escherichia coli (E. coli) / References: UniProt: P37412 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 53.45 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 15 MG/ML PROTEIN IN 0.65% AMMONIUM SULFATE 2MM MNCL2, 100 MM CITRATE PH = 5.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. obs: 68704 / % possible obs: 79 % / Redundancy: 5.9 % / Rsym value: 0.057 |
Reflection | *PLUS Num. measured all: 407579 / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1 IPD Resolution: 1.76→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.79 Å / Total num. of bins used: 18
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.411 |