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Yorodumi- PDB-6owp: Horse liver F93W alcohol dehydrogenase complexed with NAD and tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6owp | |||||||||
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Title | Horse liver F93W alcohol dehydrogenase complexed with NAD and trifluoroethanol | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / NAD / 2 / 2-trifluoretanol / Phe93 to Trp substitution / Horse liver E enzyme | |||||||||
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 / Resolution: 1.14 Å | |||||||||
Authors | Plapp, B.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2020 Title: Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer. Authors: Kim, K. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1993 Title: Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis. Authors: Bahnson, B.J. / Park, D.H. / Kim, K. / Plapp, B.V. / Klinman, J.P. #2: 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. #3: Journal: Isotope Effects in Chemistry and Biology / Year: 2006 Title: Catalysis by Alcohol Dehydrogenases Authors: Plapp, B.V. #4: 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. #5: Journal: Biochemistry / Year: 1998 Title: Active site modifications in a double mutant of liver alcohol dehydrogenase: structural studies of two enzyme-ligand complexes. Authors: Colby, T.D. / Bahnson, B.J. / Chin, J.K. / Klinman, J.P. / Goldstein, B.M. #6: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997 Title: A link between protein structure and enzyme catalyzed hydrogen tunneling. Authors: Bahnson, B.J. / Colby, T.D. / Chin, J.K. / Goldstein, B.M. / Klinman, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6owp.cif.gz | 355.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6owp.ent.gz | 287.8 KB | Display | PDB format |
PDBx/mmJSON format | 6owp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6owp_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 6owp_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 6owp_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 6owp_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/6owp ftp://data.pdbj.org/pub/pdb/validation_reports/ow/6owp | HTTPS FTP |
-Related structure data
Related structure data | 6o91C 6oa7C 6owmSC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39892.309 Da / Num. of mol.: 2 / Mutation: F93W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1035 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.38 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 Details: 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanne sulfonate, pH 6.7 (at 25 deg C), 0,25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 12-15 % 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.827 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2008 / Details: Rosenbaum-Rock vertically focussed mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→19.97 Å / Num. obs: 244957 / % possible obs: 91.2 % / Redundancy: 3.71 % / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Χ2: 1.18 / Net I/σ(I): 12.2 / Num. measured all: 914787 / Scaling rejects: 6861 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6owm Resolution: 1.14→19.97 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.896 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 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: 61.1 Å2 / Biso mean: 13.986 Å2 / Biso min: 6.94 Å2
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Refinement step | Cycle: final / Resolution: 1.14→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.14→1.17 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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