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Yorodumi- PDB-8eiy: Cobalt(II)-substituted S48T Horse Liver Alcohol Dehydrogenase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eiy | |||||||||
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Title | Cobalt(II)-substituted S48T 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: 2.55 Å | |||||||||
Authors | Zheng, C. / Mathews, I.I. / Boxer, S.G. | |||||||||
Funding support | United States, 2items
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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 | 8eiy.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eiy.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 8eiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/8eiy ftp://data.pdbj.org/pub/pdb/validation_reports/ei/8eiy | HTTPS FTP |
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-Related structure data
Related structure data | 7u9nC 7uq9C 7utwC 8eiwC 8eixC 7rm6S 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: 40052.480 Da / Num. of mol.: 2 / Mutation: S48T Source method: isolated from a genetically manipulated source Details: liver enzyme / Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 52 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CXF / | #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: 2.09 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: tert-butanol(12%-20%), 2mM NADH, 3.3mM N-cyclohexylformamide, 1mM Co(II) acetate in 50mM 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: 0.97946 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2022 Details: Rh coated collimating mirrors, K-B focusing mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→39.09 Å / Num. obs: 22067 / % possible obs: 95.7 % / Redundancy: 7.05 % / Biso Wilson estimate: 66.231 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.166 / Χ2: 0.816 / Net I/σ(I): 9.41 / Num. measured all: 155570 / Scaling rejects: 24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RM6 Resolution: 2.55→39.09 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.15 / 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: 107.84 Å2 / Biso mean: 59.1988 Å2 / Biso min: 30.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→39.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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