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- PDB-4j2h: Crystal structure of a putative short-chain alcohol dehydrogenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j2h | ||||||
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Title | Crystal structure of a putative short-chain alcohol dehydrogenase from Sinorhizobium meliloti 1021 (Target NYSGRC-011708) | ||||||
![]() | Short chain alcohol dehydrogenase-related dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / short-chain dehydrogenase / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium / dehydrogenase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. ...Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: Crystal structure of a putative short-chain alcohol dehydrogenase from Sinorhizobium meliloti 1021 (Target NYSGRC-011708) Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | 87.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27048.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG4 #82; G10: 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 20% (v/v) 2-Propanol); Cryoprotection (30% Ethylene glycol), ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG4 #82; G10: 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 20% (v/v) 2-Propanol); Cryoprotection (30% Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 19305 / Num. obs: 19305 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.7 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.075 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 42.9 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 939 / Rsym value: 0.998 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.18 Å2 / Biso mean: 61.0321 Å2 / Biso min: 33.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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