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Yorodumi- PDB-7u9n: S48A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u9n | ||||||
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Title | S48A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / Ternary complex | ||||||
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: 2.2 Å | ||||||
Authors | Zheng, C. / Boxer, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem. / Year: 2023 Title: Enhanced active-site electric field accelerates enzyme catalysis. Authors: Zheng, C. / Ji, Z. / Mathews, I.I. / Boxer, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u9n.cif.gz | 294.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u9n.ent.gz | 236.7 KB | Display | PDB format |
PDBx/mmJSON format | 7u9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/7u9n ftp://data.pdbj.org/pub/pdb/validation_reports/u9/7u9n | HTTPS FTP |
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-Related structure data
Related structure data | 7uq9C 7utwC 8eiwC 8eixC 8eiyC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40022.453 Da / Num. of mol.: 4 / Mutation: S48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-CXF / #5: Water | ChemComp-HOH / | 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: 2.16 Å3/Da / Density % sol: 42.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG400(10%-25%), 2mM NADH, and 10mM N-cyclohexylformamide in Tris buffer at pH 8.20 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→38.13 Å / Num. obs: 61757 / % possible obs: 90.6 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Net I/σ(I): 9.7 / Num. measured all: 474125 / Scaling rejects: 58 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DWV Resolution: 2.2→35.93 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.72 Å2 / Biso mean: 51.3722 Å2 / Biso min: 23.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→35.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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