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Yorodumi- PDB-5vl0: horse liver alcohol dehydrogenase complexed with NADH and N-benzy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vl0 | |||||||||
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Title | horse liver alcohol dehydrogenase complexed with NADH and N-benzyformamide | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / N-benzylformamide / horse liver / NADH | |||||||||
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 / molecular replacement / Resolution: 1.2 Å | |||||||||
Authors | Plapp, B.V. / Brown, E.N. / Ramaswamy, S. / Baskar Raj, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2017 Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S. #1: Journal: Biochemistry / Year: 2012 Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vl0.cif.gz | 626.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vl0.ent.gz | 517.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vl0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5vl0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5vl0_validation.xml.gz | 68.7 KB | Display | |
Data in CIF | 5vl0_validation.cif.gz | 101 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/5vl0 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/5vl0 | HTTPS FTP |
-Related structure data
Related structure data | 5vj5C 5vjgC 5vkrC 5vn1C 1p1rS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1365 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-BNF / #5: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.05 % / Description: long blocks |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 10 mg/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of ...Details: 10 mg/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. Crystas was mounted on a fiber loop and flash vitrified by plunging it into liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 19, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→19.95 Å / Num. obs: 365139 / % possible obs: 79.4 % / Redundancy: 6.19 % / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.094 / Χ2: 1.14 / Net I/σ(I): 8.3 / Num. measured all: 2278017 / Scaling rejects: 17086 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P1R Resolution: 1.2→19.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.849 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.049 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.67 Å2 / Biso mean: 20.318 Å2 / Biso min: 10.13 Å2
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Refinement step | Cycle: final / Resolution: 1.2→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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