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Yorodumi- PDB-6t9m: Crystal structure of the Chitinase Domain of the Spore Coat Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t9m | ||||||
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Title | Crystal structure of the Chitinase Domain of the Spore Coat Protein CotE from Clostridium difficile | ||||||
Components |
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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 | Peptoclostridium difficile (bacteria) Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 | 6t9m.cif.gz | 255.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9m ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9m | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 42924.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This is the C-terminal chitinase domain of a bifunctional protein found in the spores of Clostridium difficile. It has an HRV 3C cleavable H6 tag fused to its N-terminus Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria) Strain: 630 / Gene: cotE, CD630_14330 / Plasmid: pETYSBLLIC3C Details (production host): T7 promoter regulated by lac repressor/operator Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q18BV5, peroxiredoxin | ||||||
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#2: Protein/peptide | Mass: 503.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide defined by electron density in active site / Source: (synth.) Escherichia coli K-12 (bacteria) | ||||||
#3: Chemical | #4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Well solution: 200 mM ammonium phosphate, 22.5% PEG 3350 Protein solution: 20 mM Tris-HCl, pH 8.0, 150 mM NaCl Drop: 3 microlitre (1 microlitre protein plus 2 microlitre reservoir solution) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→47.21 Å / Num. obs: 94650 / % possible obs: 97.9 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rrim(I) all: 0.058 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 6.5 / Num. unique obs: 4564 / CC1/2: 0.954 / Rrim(I) all: 0.31 / % possible all: 96.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: xxx Resolution: 1.3→45.09 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.137 / WRfactor Rwork: 0.107 / Average fsc free: 0.9794 / Average fsc work: 0.9835 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.035 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.194 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→45.09 Å
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Refine LS restraints |
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LS refinement shell |
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