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Yorodumi- PDB-1qv7: HORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qv7 | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPLEXED WITH NAD+ AND 2,3-DIFLUOROBENZYL ALCOHOL | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / 2 / 3-DIFLUOROBENZYL ALCOHOL / HIS51GLN/LYS228ARG MUTANT / HORSE LIVER | ||||||
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: 1.8 Å | ||||||
Authors | Lebrun, L.A. / Park, D.-H. / Ramaswamy, S. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase. Authors: LeBrun, L.A. / Park, D.-H. / Ramaswamy, S. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1994 Title: Structures of Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols. Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. #2: Journal: Biochemistry / Year: 1999 Title: Control of Coenzyme Binding to Horse Liver Alcohol Dehydrogenase. Authors: LeBrun, L.A. / Plapp, B.V. #3: Journal: Biochemistry / Year: 2002 Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenase as Determined by NMR and X-Ray Crystallographic Studies. Authors: Rubach, J.K. / Plapp, B.V. #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. #6: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qv7.cif.gz | 165.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qv7.ent.gz | 128.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qv7_validation.pdf.gz | 991.9 KB | Display | wwPDB validaton report |
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Full document | 1qv7_full_validation.pdf.gz | 999.3 KB | Display | |
Data in XML | 1qv7_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 1qv7_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qv7 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qv7 | HTTPS FTP |
-Related structure data
Related structure data | 1qv6C 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: 39871.270 Da / Num. of mol.: 2 Fragment: Recombinant enzyme without the N-acetyl group found in natural enzyme Mutation: H51Q and K228R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Plasmid: pBPP / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.37 Å3/Da / Density % sol: 48.07 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: dialysis / pH: 7 Details: 50 mM ammonium N-[tris(hydroxymethyl)methyl)]-2-aminoethanesulfonate buffer, 1 mM NAD+, 10 mM 2,3-difluorobenzyl alcohol, 2-methyl-2,4-pentanediol, pH 7.0, dialysis, temperature 278K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ | ||||||||||||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 1.03 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 67918 / Num. obs: 67918 / % possible obs: 95.1 % / Redundancy: 1.95 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.06 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.72 / Num. unique all: 8849 / % possible all: 91.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 132501 |
Reflection shell | *PLUS % possible obs: 94.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hld Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.341 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / 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: 21.007 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.178 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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