+Open data
-Basic information
Entry | Database: PDB / ID: 7vo5 | ||||||
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Title | Pimaricin type I PKS thioesterase domain (holo Pim TE) | ||||||
Components | ScnS4 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / thioesterase / type I thioesterase / pimaricin / polyketide synthase thioesterase domain | ||||||
Function / homology | Function and homology information macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces chattanoogensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bai, L. / Zhou, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Structural and Mechanistic Insights into Chain Release of the Polyene PKS Thioesterase Domain Authors: Zhou, Y. / Tao, W. / Qi, Z. / Wei, J. / Shi, T. / Kang, Q. / Zheng, J. / Zhao, Y. / Bai, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vo5.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vo5.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/7vo5 ftp://data.pdbj.org/pub/pdb/validation_reports/vo/7vo5 | HTTPS FTP |
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-Related structure data
Related structure data | 7vo4SC 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: 30898.953 Da / Num. of mol.: 1 / Fragment: pimaricin type I PKS thioesterase domain (Pim TE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces chattanoogensis (bacteria) Gene: scnS4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F1CLA7 |
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#2: Chemical | ChemComp-81E / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 1.5M Sodium citrate tribasic dihydrate PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→82.66 Å / Num. obs: 20938 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.032 / Rrim(I) all: 0.102 / Χ2: 0.986 / Net I/σ(I): 5.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VO4 Resolution: 2.4→82.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.15 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.187 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.49 Å2 / Biso mean: 45.253 Å2 / Biso min: 18.07 Å2
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Refinement step | Cycle: final / Resolution: 2.4→82.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.459 Å / Rfactor Rfree error: 0
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