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Yorodumi- PDB-5kj1: G173A horse liver alcohol dehydrogenase complexed with NAD+ and p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kj1 | ||||||
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Title | G173A horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE Inhibitor complex Rossmann fold dynamics | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / ethanol oxidation / 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. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Authors: Plapp, B.V. / Gakhar, L. / Subramanian, R. #1: Journal: Protein Sci. / Year: 2018 Title: Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Authors: Shanmuganatham, K.K. / Wallace, R.S. / Ting-I Lee, A. / Plapp, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kj1.cif.gz | 349.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kj1.ent.gz | 282.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kj1 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kj1 | HTTPS FTP |
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-Related structure data
Related structure data | 4dwvS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/900 / 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: 39867.301 Da / Num. of mol.: 2 / Mutation: G173A Source method: isolated from a genetically manipulated source Details: G173A substitution / Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1Blue / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1028 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MRD / ( #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: 2.26 Å3/Da / Density % sol: 46 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL |
-Data collection
Diffraction | Mean temperature: 85 K / Ambient temp details: Helium cryostat |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2009 Details: ROSENBAUM ROCK VERTICAL FOCUSING MIRROR WITH PT, GLASS, PD LANES |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 220050 / % possible obs: 94.6 % / Redundancy: 3.95 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.1 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DWV Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.44 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.037 / 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: 16.997 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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