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Yorodumi- PDB-5kcp: horse liver S48T alcohol dehydrogenase complexed with NAD and pen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kcp | ||||||
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Title | horse liver S48T alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / Ser48 to Thr-48 substitution / Horse Liver Alcohol Dehydrogenase / NAD-pentafluorobenzyl alcohol | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Plapp, B.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem. Biol. Interact. / Year: 2017 Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93. Authors: Kim, K. / 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 | 5kcp.cif.gz | 347.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kcp.ent.gz | 281.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kcp_validation.pdf.gz | 975.9 KB | Display | wwPDB validaton report |
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Full document | 5kcp_full_validation.pdf.gz | 979.4 KB | Display | |
Data in XML | 5kcp_validation.xml.gz | 40 KB | Display | |
Data in CIF | 5kcp_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kcp ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kcp | HTTPS FTP |
-Related structure data
Related structure data | 5kczC 4dwvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/662 / 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: S48T Source method: isolated from a genetically manipulated source Details: horse liver alcohol dehydrogenase E isoenzyme with S48T substitution Source: (gene. exp.) Equus caballus (horse) / Organ: Liver / Plasmid: pBPP/EqADH / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1057 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-PFB / #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: 2.28 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+, 100 mM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: ADJUSTABLE FOCUS K-B PAIR SIPLUS PT, RH COATINGS |
Radiation | Monochromator: DOUBLE CRYSTAL CRYOCOOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→19.4 Å / Num. obs: 270420 / % possible obs: 89.3 % / Redundancy: 5.52 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.1 / % possible all: 56.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DWV Resolution: 1.1→19.4 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.701 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / 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: 16.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→19.4 Å
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Refine LS restraints |
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