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Yorodumi- PDB-5vj5: Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vj5 | |||||||||
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Title | Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / 1 / 10-phenanthroline / zinc chelation / liver / apoenzyme | |||||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Plapp, B.V. / Baskar Raj, S. / Ramaswamy, 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: Eur. J. Biochem. / Year: 1977 Title: X-ray investigation of the binding of 1,10-phenanthroline and imidazole to horse-liver alcohol dehydrogenase. Authors: Boiwe, T. / Branden, C.I. #2: 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 | 5vj5.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vj5.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vj5 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vj5 | HTTPS FTP |
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-Related structure data
Related structure data | 5vjgC 5vkrC 5vl0C 5vn1C 1ju9S 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: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 8.4 Details: 50 mM Tris-HCl, pH 8.4, 10 mg protein/ml in dialysis bag, dialyzed against 2-methyl-2,4-pentanediol, raised slowly to 25 %. Crystals soaked with 5 mM 1,10-phenanthroline for 2 hr at 278K, ...Details: 50 mM Tris-HCl, pH 8.4, 10 mg protein/ml in dialysis bag, dialyzed against 2-methyl-2,4-pentanediol, raised slowly to 25 %. Crystals soaked with 5 mM 1,10-phenanthroline for 2 hr at 278K, and flash vitrified in liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2005 / Details: MSC Yale confocal Osmic |
Radiation | Monochromator: flat graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 55508 / % possible obs: 96.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.97 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5486 / Χ2: 1.15 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JU9 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.898 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.186 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: 101.79 Å2 / Biso mean: 35.539 Å2 / Biso min: 19.13 Å2
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Refinement step | Cycle: final / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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