+Open data
-Basic information
Entry | Database: PDB / ID: 5l40 | ||||||||||||
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Title | polyketide ketoreductase SimC7 - apo crystal form 1 | ||||||||||||
Components | polyketide ketoreductase SimC7 | ||||||||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase/reductase / Ketoreductase / Simocyclinone / DNA gyrase inhibitor | ||||||||||||
Function / homology | NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative hydroxylase/dehydratase Function and homology information | ||||||||||||
Biological species | Streptomyces antibioticus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 5l40.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l40.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l40_validation.pdf.gz | 417.5 KB | Display | wwPDB validaton report |
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Full document | 5l40_full_validation.pdf.gz | 417.7 KB | Display | |
Data in XML | 5l40_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5l40_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/5l40 ftp://data.pdbj.org/pub/pdb/validation_reports/l4/5l40 | HTTPS FTP |
-Related structure data
Related structure data | 5l3zSC 5l45C 5l4lC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 construct named pET15b-NB-C7 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: 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: 2.27 Å3/Da / Density % sol: 45.81 % |
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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: I04-1 / Wavelength: 0.9173 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 26, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.6→53.4 Å / Num. obs: 40514 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.069 / Net I/σ(I): 20 / Num. measured all: 435288 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L3Z Resolution: 1.6→53.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.002 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0861 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087 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: 83.87 Å2 / Biso mean: 34.56 Å2 / Biso min: 14.65 Å2
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Refinement step | Cycle: final / Resolution: 1.6→53.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 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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