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Yorodumi- PDB-2cfc: structural basis for stereo selectivity in the (R)- and (S)- hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cfc | ||||||
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Title | structural basis for stereo selectivity in the (R)- and (S)- hydroxypropylethane thiosulfonate dehydrogenases | ||||||
Components | 2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE2-(R)-hydroxypropyl-CoM dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD | ||||||
Function / homology | Function and homology information 2-(R)-hydroxypropyl-CoM dehydrogenase / 2-(R)-hydroxypropyl-CoM dehydrogenase activity / propylene catabolic process Similarity search - Function | ||||||
Biological species | XANTHOBACTER AUTOTROPHICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Krishnakumar, A.M. / Nocek, B.P. / Clark, D.D. / Ensign, S.A. / Peters, J.W. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structural Basis for Stereoselectivity in the (R)-and (S)-Hydroxypropylthioethanesulfonate Dehydrogenases. Authors: Krishnakumar, A.M. / Nocek, B.P. / Clark, D.D. / Ensign, S.A. / Peters, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cfc.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cfc.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/2cfc ftp://data.pdbj.org/pub/pdb/validation_reports/cf/2cfc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: (1), |
-Components
#1: Protein | Mass: 26165.854 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) XANTHOBACTER AUTOTROPHICUS (bacteria) / Strain: PY2 References: UniProt: Q56840, 2-(R)-hydroxypropyl-CoM dehydrogenase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-KPC / ( #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: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Details: 15MM NAD, 0.2M MAGNESIUM CHLORIDE, 0.1 M HEPES, PH7.5, 30% W/V PEG400 AND 0.1 SPERMINE TETRACHLORIDE AND 20MM R-HYDROXY PROPYL COM |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.87008,1.00871 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS | |||||||||
Radiation | Monochromator: NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→20 Å / Num. obs: 149113 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5 | |||||||||
Reflection shell | Highest resolution: 1.8 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 78.8068 Å2 / ksol: 0.384731 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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Xplor file |
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