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Yorodumi- PDB-6vap: Structure of the type II thioesterase BorB from the borrelidin bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vap | ||||||
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Title | Structure of the type II thioesterase BorB from the borrelidin biosynthetic cluster | ||||||
Components | Thioesterase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / thioesterase | ||||||
Function / homology | Thioesterase type II, NRPS/PKS/S-FAS / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / hydrolase activity, acting on ester bonds / biosynthetic process / Alpha/Beta hydrolase fold / Thioesterase Function and homology information | ||||||
Biological species | Streptomyces sp. WAC02707 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Pereira, J.H. / Curran, S.C. / Baluyot, M.-J. / Lake, J. / Putz, H. / Rosenburg, D. / Keasling, J. / Adams, P.D. | ||||||
Citation | Journal: Biochemistry / Year: 2020 Title: Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Authors: Curran, S.C. / Pereira, J.H. / Baluyot, M.J. / Lake, J. / Puetz, H. / Rosenburg, D.J. / Adams, P. / Keasling, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vap.cif.gz | 296.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vap.ent.gz | 236.2 KB | Display | PDB format |
PDBx/mmJSON format | 6vap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vap_validation.pdf.gz | 249.3 KB | Display | wwPDB validaton report |
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Full document | 6vap_full_validation.pdf.gz | 249.3 KB | Display | |
Data in XML | 6vap_validation.xml.gz | 924 B | Display | |
Data in CIF | 6vap_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/6vap ftp://data.pdbj.org/pub/pdb/validation_reports/va/6vap | HTTPS FTP |
-Related structure data
Related structure data | 3flaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29387.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. WAC02707 (bacteria) / Gene: EF919_13485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A454WD44 #2: 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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium Chloride, 0.1 M Hepes pH 7.5, 22% Poly (acrylic acid sodium salt) 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→46.23 Å / Num. obs: 39997 / % possible obs: 95.3 % / Redundancy: 8 % / Biso Wilson estimate: 27.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.07 |
Reflection shell | Resolution: 1.89→1.96 Å / Num. unique obs: 3844 / CC1/2: 0.874 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FLA Resolution: 1.93→46.18 Å / SU ML: 0.3022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3122 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→46.18 Å
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Refine LS restraints |
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LS refinement shell |
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