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Yorodumi- PDB-4dxh: Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dxh | ||||||
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Title | Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-trifluoroethanol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / ALCOHOL DEHYDROGENASE / NAD+ / TRIFLUOROETHANOL / MICHAELIS COMPLEX ROSSMANN FOLD | ||||||
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: 1.12 Å | ||||||
Authors | Plapp, B.V. / Ramaswamy, S. | ||||||
Citation | 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. #1: 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. #2: Journal: Biochemistry / Year: 2003 Title: Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase. Authors: Rubach, J.K. / Plapp, B.V. #3: Journal: J.Biol.Chem. / Year: 2003 Title: Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism. Authors: Venkataramaiah, T.H. / 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 | 4dxh.cif.gz | 346.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dxh.ent.gz | 280.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/4dxh ftp://data.pdbj.org/pub/pdb/validation_reports/dx/4dxh | HTTPS FTP |
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-Related structure data
Related structure data | 4dwvC 1hldS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/890 / 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: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Liver / Source: (natural) Equus caballus (horse) / Organ: liver / Strain: Domestic horse / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1037 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: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 6.7 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+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4- ...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+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL, TEMPERATURE 278K, MICRODIALYSIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 | Monochromator: Rosenbaum Rock high resolution double crystal monochromator, LN2 cooled, sagittal focussing 2nd mirror, Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→20 Å / Num. all: 283954 / Num. obs: 267668 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.1 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1HLD Resolution: 1.12→20 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.94 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / 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: 13.289 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.12→1.149 Å / Total num. of bins used: 20
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