[English] 日本語
Yorodumi- PDB-5kcz: horse liver S48T alcohol dehydrogenase complexed with NAD and tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kcz | ||||||
---|---|---|---|---|---|---|---|
Title | horse liver S48T alcohol dehydrogenase complexed with NAD and trifluoroethanol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / Ser48 to Thr-48 substitution / Horse Liver Alcohol Dehydrogenase / NAD-trifluoroethanol | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Plapp, B.V. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Chem. Biol. Interact. / Year: 2017 Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93. Authors: Kim, K. / Plapp, B.V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kcz.cif.gz | 345.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kcz.ent.gz | 280 KB | Display | PDB format |
PDBx/mmJSON format | 5kcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kcz ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kcz | HTTPS FTP |
---|
-Related structure data
Related structure data | 5kcpC 4dwvS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39867.301 Da / Num. of mol.: 2 / Mutation: S48T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Plasmid: pBPP/EqADH / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase |
---|
-Non-polymers , 5 types, 1040 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MRD / ( #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 46 % / Description: block |
---|---|
Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminomethane sulfonate, pH 7.0 (pH 6.7 at 25 C), 0.25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 100 mM trifluoroethanol, 12-25 % 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.827 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Feb 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.827 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→20 Å / Num. obs: 244846 / % possible obs: 90.7 % / Redundancy: 3.72 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.14→1.17 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.372 / % possible all: 54.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DWV Resolution: 1.14→20 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.97 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.897 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|