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Yorodumi- PDB-2bvm: Crystal structure of the catalytic domain of toxin B from Clostri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bvm | ||||||
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Title | Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion | ||||||
Components | TOXIN B | ||||||
Keywords | TOXIN / GLYCOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM DIFFICILE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Reinert, D.J. / Jank, T. / Aktories, K. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural Basis for the Function of Clostridium Difficile Toxin B. Authors: Reinert, D.J. / Jank, T. / Aktories, K. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bvm.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bvm.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bvm ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bvm | HTTPS FTP |
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-Related structure data
Related structure data | 2bvlC 2bv1S C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 62924.379 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-541 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: VPI 10463 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P18177, Transferases; Glycosyltransferases; Hexosyltransferases |
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#4: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 132 molecules
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-UDP / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 58 TO CYS ENGINEERED RESIDUE IN CHAIN A, GLU 243 TO GLY ...ENGINEERED |
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Sequence details | STRUCTURE OF MUTANT Y58C-E241G-S541A |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.82 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2003 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 24594 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.55→2.61 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BV1 Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 19.1 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.474 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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