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Yorodumi- PDB-6tsb: Crystal structure of the Chitinase Domain of the Spore Coat Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tsb | ||||||
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Title | Crystal structure of the Chitinase Domain of the Spore Coat Protein CotE from Clostridium difficile | ||||||
Components | Peroxiredoxin | ||||||
Keywords | STRUCTURAL PROTEIN / Spore Coat / Chitinase / Colonisation Factor | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Whittingham, J.L. / Dodson, E.J. / Wilkinson, A.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Crystal structures of the GH18 domain of the bifunctional peroxiredoxin-chitinase CotE from Clostridium difficile. Authors: Whittingham, J.L. / Hanai, S. / Brannigan, J.A. / Ferreira, W.T. / Dodson, E.J. / Turkenburg, J.P. / Cartwright, J. / Cutting, S.M. / Wilkinson, A.J. #1: Journal: J. Infect. Dis. / Year: 2017 Title: The Spore Coat Protein CotE Facilitates Host Colonization by Clostridium difficile. Authors: Hong, H.A. / Ferreira, W.T. / Hosseini, S. / Anwar, S. / Hitri, K. / Wilkinson, A.J. / Vahjen, W. / Zentek, J. / Soloviev, M. / Cutting, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tsb.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tsb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tsb_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
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Full document | 6tsb_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 6tsb_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6tsb_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/6tsb ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6tsb | HTTPS FTP |
-Related structure data
Related structure data | 6t9mSC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40771.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (strain 630) (bacteria) Gene: cotE, CD630_14330 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q18BV5, peroxiredoxin | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Reservoir, 1 ml 0.1 M sodium malonate pH 5.5, 13% PEG 3,350 and 3 microlitres of pentaethylene glycol monooctyl ether (C8E5) Drops contained 2 microlitres of protein at 20 mg/ml in 50 mM ...Details: Reservoir, 1 ml 0.1 M sodium malonate pH 5.5, 13% PEG 3,350 and 3 microlitres of pentaethylene glycol monooctyl ether (C8E5) Drops contained 2 microlitres of protein at 20 mg/ml in 50 mM Tris-HCl, pH 7.5, 500 mM NaCl, 10 mM imidazole, a 3 microlitres of reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→81.41 Å / Num. obs: 35657 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 1 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.17→2.17 Å / Num. unique obs: 2551 / CC1/2: 0.64 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6T9M Resolution: 2.1→54.373 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.158 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.348 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→54.373 Å
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Refine LS restraints |
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LS refinement shell |
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