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Yorodumi- PDB-3wg6: Crystal structure of conjugated polyketone reductase C1 from Cand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wg6 | ||||||
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Title | Crystal structure of conjugated polyketone reductase C1 from Candida parapsilosis complexed with NADPH | ||||||
Components | Conjugated polyketone reductase C1 | ||||||
Keywords | OXIDOREDUCTASE / AKR SUPERFAMILY / TIM BARREL / D-PANTOYL LACTONE | ||||||
Function / homology | Function and homology information 2-dehydropantolactone reductase (Re-specific) / 2-dehydropantolactone reductase (A-specific) activity / cellular ketone metabolic process Similarity search - Function | ||||||
Biological species | Candida parapsilosis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Qin, H.-M. / Yamamura, A. / Miyakawa, T. / Maruoka, S. / Ohtsuka, J. / Nagata, K. / Kataoka, M. / Shimizu, S. / Tanokura, M. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH. Authors: Qin, H.M. / Yamamura, A. / Miyakawa, T. / Kataoka, M. / Maruoka, S. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wg6.cif.gz | 479 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wg6.ent.gz | 403.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/3wg6 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/3wg6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 34821.184 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida parapsilosis (yeast) / Strain: IFO 0708 / Gene: cpr-c1 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q76L37 #2: Chemical | ChemComp-NDP / #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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 5MM NADPH, 0.1M TRIS-HCL, 25% PEG 3350, 5MM NACL, PH 8.5, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 67499 / % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.719 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.78 Å
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Refine LS restraints |
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