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Yorodumi- PDB-4dc1: Crystal Structure of Y202F Actinorhodin Polyketide Ketoreductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dc1 | ||||||
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Title | Crystal Structure of Y202F Actinorhodin Polyketide Ketoreductase with NADPH | ||||||
Components | Ketoacyl reductase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / short-chain dehydrogenase/reductase / ketoreductase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / antibiotic biosynthetic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | ||||||
Authors | Javidpour, P. / Tsai, S.-C. | ||||||
Citation | Journal: Chem.Biol. / Year: 2013 Title: The Determinants of Activity and Specificity in Actinorhodin Type II Polyketide Ketoreductase. Authors: Javidpour, P. / Bruegger, J. / Srithahan, S. / Korman, T.P. / Crump, M.P. / Crosby, J. / Burkart, M.D. / Tsai, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dc1.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dc1.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dc1 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dc1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29448.365 Da / Num. of mol.: 2 / Mutation: Y202F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: actIII, SCBAC28G1.12c, SCO5086 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P16544, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: 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: 3.28 Å3/Da / Density % sol: 62.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.1 M Bis-Tris Propane, 2.6 M ammonium sulfate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→50 Å / Num. obs: 18227 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→42.373 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 21.7 / 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 / Bsol: 37.362 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.82→42.373 Å
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Refine LS restraints |
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LS refinement shell |
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