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Yorodumi- PDB-1qlh: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NAD DOUBLE MUTANT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qlh | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NAD DOUBLE MUTANT OF GLY 293 ALA AND PRO 295 THR | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / DOUBLE MUTANT | ||||||
Function / homology | Function and homology information : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | EQUUS CABALLUS (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Ramaswamy, S. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Substitutions in the Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V. #1: Journal: J.Biol.Chem. / Year: 1982 Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I. #2: 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. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #3: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qlh.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qlh.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qlh_validation.pdf.gz | 711.2 KB | Display | wwPDB validaton report |
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Full document | 1qlh_full_validation.pdf.gz | 715.5 KB | Display | |
Data in XML | 1qlh_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1qlh_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1qlh ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1qlh | HTTPS FTP |
-Related structure data
Related structure data | 1qljC 1hldS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 39871.289 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) EQUUS CABALLUS (horse) / Description: E.COLI EXPRESSED MUTANT PROTEIN / Cellular location: CYTOPLASM / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CJ236 / References: UniProt: P00327, alcohol dehydrogenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Water | ChemComp-HOH / | Sequence details | MUTANT PROTEIN SEQUENCE NOT SUBMITTED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / pH: 7 / 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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→20 Å / Num. obs: 18016 / % possible obs: 79.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 19.31 Å2 / Rsym value: 0.112 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.314 / % possible all: 57.4 |
Reflection | *PLUS Num. measured all: 44823 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 57.4 % / Rmerge(I) obs: 0.301 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLD Resolution: 2.07→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD ON F'S
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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