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Yorodumi- PDB-1n8k: Horse Liver Alcohol Dehydrogenase Val292Thr Mutant Complexed to N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n8k | ||||||
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Title | Horse Liver Alcohol Dehydrogenase Val292Thr Mutant Complexed to NAD+ and Pyrazole | ||||||
Components | Alcohol Dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / MUTANT / PYRAZOLE | ||||||
Function / homology | Function and homology information alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / NAD-retinol dehydrogenase activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | ||||||
Authors | Rubach, J.K. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Amino Acid Residues in the Nicotinamide Binding Site Contribute to Catalysis by Horse Liver Alcohol Dehydrogenase Authors: Rubach, J.K. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1982 Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.P. / Wallen, L. #2: Journal: J.Biol.Chem. / Year: 1996 Title: X-Ray Structure of Human beta3beta3 Alcohol Dehydrogenase. The contribution of ionic interactions to coenzyme binding. Authors: Davis, G.J. / Bosron, W.F. / Stone, C.L. / Owusu-Dekyi, K. / Hurley, T.D. #3: Journal: J.Mol.Biol. / Year: 1994 Title: Structures of Three Human Beta Alcohol Dehydrogenase Variants. Correlations with their Functional Differences. Authors: Hurley, T.D. / Bosron, W.F. / Stone, C.L. / Amzel, L.M. #4: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of A Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution Authors: Eklund, H. / Samama, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #5: Journal: J.Mol.Biol. / Year: 1976 Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. | ||||||
History |
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Remark 600 | HETEROGEN THE STRUCTURE DETERMINED IN THIS ENTRY CONTAINS THE HETEROATOM MOLECULE NAJ, WHICH IS ...HETEROGEN THE STRUCTURE DETERMINED IN THIS ENTRY CONTAINS THE HETEROATOM MOLECULE NAJ, WHICH IS OXIDIZED NICOTINAMIDE ADENINE DINUCLEOTIDE, BUT THE RESTRAINTS ON THE PLANARITY OF THE NICOTINAMIDE RING WERE REMOVED DURING REFINEMENT WITH THE RESULT THAT THE RING IS PUCKERED. | ||||||
Remark 285 | CRYST1 TO GENERATE THE STANDARD UNIT CELL FOR P1 FROM THE CELL DESCRIBED IN THE CRYST CARD, APPLY ...CRYST1 TO GENERATE THE STANDARD UNIT CELL FOR P1 FROM THE CELL DESCRIBED IN THE CRYST CARD, APPLY THE FOLLOWING: 0.000000 1.000000 0.000000 0.00000 0.000000 0.000000 1.000000 0.00000 1.000000 0.000000 0.000000 0.00000 WHICH YIELDS THE FOLLOWING UNIT CELL PARAMETERS: 51.4 92.7 44.3 103.0 109.9 91.9 P 1 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n8k.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n8k.ent.gz | 245.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n8k ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n8k | HTTPS FTP |
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-Related structure data
Related structure data | 1n92C 1hldS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39855.246 Da / Num. of mol.: 2 / Mutation: V292T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: ADHE M64864 / Plasmid: PBPP / Production host: Escherichia coli (E. coli) / Strain (production host): CJ236 / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 716 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: 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: 2.13 Å3/Da / Density % sol: 41.89 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 7 / Details: MPD, pH 7.0, dialysis, temperature 277K, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→20 Å / Num. obs: 218390 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.058 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.13→1.16 Å / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.172 / % possible all: 46.2 |
Reflection | *PLUS Highest resolution: 1.13 Å / Lowest resolution: 20 Å / % possible obs: 81.6 % / Num. measured all: 6143593 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 46.2 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 6.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLD Resolution: 1.13→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.489 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.194 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.13→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.131→1.161 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.167 / Rfactor Rwork: 0.145 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.19 |