+Open data
-Basic information
Entry | Database: PDB / ID: 3sju | ||||||
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Title | Hedamycin Polyketide Ketoreductase bound to NADPH | ||||||
Components | Keto reductase | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase / reductase / Rossmann Fold / Type II Polyketide Ketoreductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseoruber (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Javidpour, P. / Tsai, S.-C. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structural and Biochemical Studies of the Hedamycin Type II Polyketide Ketoreductase (HedKR): Molecular Basis of Stereo- and Regiospecificities. Authors: Javidpour, P. / Das, A. / Khosla, C. / 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 | 3sju.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sju.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 3sju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sju ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sju | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28959.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoruber (bacteria) / Gene: hedA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67G28 #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 grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M imidazole pH 6.2, 50% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→50 Å / Num. obs: 15891 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Χ2: 1.195 / Net I/σ(I): 13.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 46.59 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2629 / WRfactor Rwork: 0.1919 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8166 / SU B: 9.241 / SU ML: 0.219 / SU Rfree: 0.3066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 110.39 Å2 / Biso mean: 48.407 Å2 / Biso min: 24.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.402→2.464 Å / Total num. of bins used: 20
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