+Open data
-Basic information
Entry | Database: PDB / ID: 5l3z | ||||||||||||
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Title | polyketide ketoreductase SimC7 - binary complex with NADP+ | ||||||||||||
Components | polyketide ketoreductase SimC7 | ||||||||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase/reductase / Ketoreductase / Simocyclinone / DNA gyrase inhibitor | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptomyces antibioticus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å | ||||||||||||
Authors | Schafer, M. / Stevenson, C.E.M. / Wilkinson, B. / Lawson, D.M. / Buttner, M.J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Cell Chem Biol / Year: 2016 Title: Substrate-Assisted Catalysis in Polyketide Reduction Proceeds via a Phenolate Intermediate. Authors: Schafer, M. / Stevenson, C.E. / Wilkinson, B. / Lawson, D.M. / Buttner, M.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l3z.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l3z.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 5l3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/5l3z ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l3z | 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: 32277.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A twenty residue nickel affinity tag with sequence MGSSHHHHHHSSGLVPRGSH was appended to the N-terminus of the native amino acid sequence being derived from the pET-15b vector Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: simC7 / Plasmid: pET15b-NB-C7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: G9VYV4 |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0052 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0052 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.95→50.74 Å / Num. obs: 22650 / % possible obs: 99.9 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Net I/σ(I): 18.4 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SIRAS |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.95→50.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.886 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1515 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.139 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.94 Å2 / Biso mean: 46.391 Å2 / Biso min: 19.77 Å2
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Refinement step | Cycle: final / Resolution: 1.95→50.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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