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Yorodumi- PDB-8g4v: Horse liver alcohol dehydrogense His-51-Gln form complexed with N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g4v | ||||||
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Title | Horse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase horse liver His-51- Gln substitution / complex with NAD+ and pentafluorobenzyl alcohol | ||||||
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: 1.2 Å | ||||||
Authors | Plapp, B.V. / Subramanian, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Histidine-51 facilitates deprotonation of the zinc-bound ligand during catalysis by horse liver alcohol dehydrogenase Authors: Plapp, B.V. / Kovaleva, E.G. #1: 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. #2: Journal: Biochemistry / Year: 2004 Title: Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase. Authors: LeBrun, L.A. / Park, D.H. / Ramaswamy, S. / Plapp, B.V. #3: Journal: Ph.D. Thesis / Year: 2004 Title: Proton Transfer In The Mechanism Of Horse Liver Alcohol Dehydrogenase Authors: Kovaleva, E.G. #4: Journal: Biochemistry / Year: 1999 Title: Control of coenzyme binding to horse liver alcohol dehydrogenase. Authors: Plapp, B.V. / LeBrun, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g4v.cif.gz | 329.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g4v.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 8g4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/8g4v ftp://data.pdbj.org/pub/pdb/validation_reports/g4/8g4v | HTTPS FTP |
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-Related structure data
Related structure data | 8g2lC 8g2sC 8g2xC 8g39C 4dwvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 39843.258 Da / Num. of mol.: 2 / Mutation: H51Q 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, 682 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.28 Å3/Da / Density % sol: 46 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ...Details: 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ~13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→19.96 Å / Num. obs: 211946 / % possible obs: 91.1 % / Redundancy: 6.13 % / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 1.1 / Net I/σ(I): 13.3 / Num. measured all: 1316799 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4dwv Resolution: 1.2→19.96 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.118 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.445 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→19.96 Å
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Refine LS restraints |
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