[English] 日本語
Yorodumi- PDB-1bto: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND (1S,3R)3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bto | ||||||
---|---|---|---|---|---|---|---|
Title | HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND (1S,3R)3-BUTYLTHIOLANE 1-OXIDE | ||||||
Components | LIVER ALCOHOL DEHYDROGENASEAlcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ALCOHOL / NICOTINAMIDE COENZYME / SULFOXIDE | ||||||
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: 2 Å | ||||||
Authors | Ramaswamy, S. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides. Authors: Cho, H. / Ramaswamy, S. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bto.cif.gz | 318.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bto.ent.gz | 260.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/1bto ftp://data.pdbj.org/pub/pdb/validation_reports/bt/1bto | HTTPS FTP |
---|
-Related structure data
Related structure data | 3btoC 1hldS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: COMMERCIAL PREPARATION OF ENZYME FROM HORSE LIVER. CDNA SEQUENCE M64864 Source: (natural) Equus caballus (horse) / Cellular location: CYTOPLASM / Organ: LIVER / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-SSB / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: batch dialysis / pH: 7 Details: THE 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. ...Details: THE 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 3-BUTYLTHIOLANE 1-OXIDE., batch dialysis | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 78371 / % possible obs: 79 % / Redundancy: 2 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.043 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.152 / % possible all: 31 |
Reflection | *PLUS Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 31 % / Rmerge(I) obs: 0.152 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLD Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: STRUCTURE WAS REFINED WITH NCS RESTRAINTS -TIGHT CLASS. FOR THE BEST REFINED STRUCTURE OF ADH FROM THE DEPOSITORS' LAB USE COORDINATES OF PEAK 3 OF BTO COMPLEX.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |