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Yorodumi- PDB-8g2l: Horse liver alcohol dehydrogense His-51 Gln form complexed with N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g2l | ||||||
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Title | Horse liver alcohol dehydrogense His-51 Gln form complexed with NAD+ and 2,2,2-trifluoroethanol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase horse liver His-48 Gln substitution complex with NAD+ and trifluoroethanol | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Plapp, B.V. | ||||||
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 | 8g2l.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g2l.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 8g2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g2l_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 8g2l_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 8g2l_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 8g2l_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/8g2l ftp://data.pdbj.org/pub/pdb/validation_reports/g2/8g2l | HTTPS FTP |
-Related structure data
Related structure data | 8g2sC 8g2xC 8g39C 8g4vC 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) / Tissue: liver / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 6 types, 678 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MRD / ( | #7: 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: 2.26 Å3/Da / Density % sol: 45 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: batch mode / pH: 7 Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminiomethanesulfonate and 0.25 mM EDTA, 2 mM NAD+, 0.1 mM 2,2,2-trifluoroetanol, 13% MPD, crystals soaked with 25% MPD, and ...Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminiomethanesulfonate and 0.25 mM EDTA, 2 mM NAD+, 0.1 mM 2,2,2-trifluoroetanol, 13% MPD, crystals soaked with 25% MPD, and 100 mM trifluoroethanol Temp details: oH 6,7 at 298 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2004 / Details: confocal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphie / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→19.87 Å / Num. obs: 121088 / % possible obs: 87.2 % / Redundancy: 6.16 % / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.18 / Net I/σ(I): 17.2 / Num. measured all: 751297 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→19.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.434 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / 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: 21.355 Å2
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Refinement step | Cycle: 1 / Resolution: 1.42→19.88 Å
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Refine LS restraints |
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