[English] 日本語
Yorodumi- PDB-5vkr: Horse liver alcohol dehydrogenase complexed with adenosine-5-diph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vkr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Horse liver alcohol dehydrogenase complexed with adenosine-5-diphosphoribose | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / horse liver / ADPR / adenosine-5-diphosphoribose / zinc | |||||||||
Function / homology | Function and homology information : / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Plapp, B.V. / Rubach, J.K. / Ramaswamy, S. | |||||||||
Funding support | United States, 2items
| |||||||||
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: 1975 Title: The conformation of adenosine diphosphoribose and 8-bromoadenosine diphosphoribose when bound to liver alcohol dehydrogenase. Authors: Abdallah, M.A. / Biellmann, J.F. / Nordstrom, B. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vkr.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vkr.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vkr_validation.pdf.gz | 737.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5vkr_full_validation.pdf.gz | 739.4 KB | Display | |
Data in XML | 5vkr_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5vkr_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vkr ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vkr | HTTPS FTP |
-Related structure data
Related structure data | 5vj5C 5vjgC 5vl0C 5vn1C 8adhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-APR / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: needles |
---|---|
Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 8.4 Details: 10 mg/ml protein in dialysis bag dialyzed against 50 mM Tris-HCl, pH 8.4 as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. A crystal was soaked with 2 mM adenosine-5- ...Details: 10 mg/ml protein in dialysis bag dialyzed against 50 mM Tris-HCl, pH 8.4 as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. A crystal was soaked with 2 mM adenosine-5-diphosphoribose in the final outer dialysate for 1 hr. Crystal flash vitrified by plunging it into liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0093 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2001 / Details: Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 30816 / % possible obs: 91.7 % / Redundancy: 7.64 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.117 / Χ2: 1.16 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.68 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2947 / Χ2: 1.23 / % possible all: 84.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8ADH Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.514 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.595 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|