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Yorodumi- PDB-6owm: Horse liver F93W alcohol dehydrogenase complexed with NAD and pen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6owm | |||||||||
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Title | Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / NAD / pentafluorobenzyl alcohol / Phe93 to Trp substitution / Horse liver E enzyme | |||||||||
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: 1.1 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 | 6owm.cif.gz | 358.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6owm.ent.gz | 289.6 KB | Display | PDB format |
PDBx/mmJSON format | 6owm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/6owm ftp://data.pdbj.org/pub/pdb/validation_reports/ow/6owm | HTTPS FTP |
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-Related structure data
Related structure data | 6o91SC 6oa7C 6owpC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/661 / Data set type: diffraction image 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) / 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: 2.41 Å3/Da / Density % sol: 48.91 % / Description: block |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethane sulfonate, 0.25 mM EDTA, pH 6.7 at 25 deg C, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 14 to 25 % 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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: adjustable foculs K-B pari SiPlus PT, RH coatings | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal cryocooled Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→19.62 Å / Num. obs: 267734 / % possible obs: 88.6 % / Redundancy: 5.15 % / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.082 / Χ2: 1.15 / Net I/σ(I): 11.4 / Num. measured all: 1394329 / Scaling rejects: 16553 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6o91 Resolution: 1.1→19.62 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.742 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 15.811 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→19.62 Å
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Refine LS restraints |
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