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Yorodumi- PDB-5tii: Comprehensive Analysis of a Novel Ketoreductase for Pentangular P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tii | ||||||
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Title | Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis | ||||||
Components | 3-oxoacyl-ACP reductase3-oxoacyl-(acyl-carrier-protein) reductase | ||||||
Keywords | OXIDOREDUCTASE / Arixanthomycin / Pentangular polyphenol Polyketide / Ketoreduction | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Valentic, T.R. / Tsai, S.C. / Brady, S.F. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2016 Title: Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis. Authors: Valentic, T.R. / Jackson, D.R. / Brady, S.F. / 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 | 5tii.cif.gz | 371.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tii.ent.gz | 304 KB | Display | PDB format |
PDBx/mmJSON format | 5tii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tii ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tii | HTTPS FTP |
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-Related structure data
Related structure data | 5thqC 1vl8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29059.971 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: arx21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023PKG5 #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: 1.99 Å3/Da / Density % sol: 38.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Acetate and 30-32% PEG 4000 / Temp details: Room temp. At UCI Natural Sciences I Rm 2302 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99.66 Å / Num. obs: 54103 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.6→2.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.932 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VL8 Resolution: 2.6→52.671 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.31 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→52.671 Å
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Refine LS restraints |
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LS refinement shell |
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