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Yorodumi- PDB-2j3x: Crystal structure of the enzymatic component C2-I of the C2-toxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j3x | ||||||
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Title | Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 3.0 (mut-S361R) | ||||||
Components | C2 TOXIN COMPONENT I | ||||||
Keywords | TOXIN / ADP-RIBOSYLTRANSFERASE / CLOSTRIDIUM BOTULINUM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CLOSTRIDIUM BOTULINUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Schleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure and Action of the Binary C2 Toxin from Clostridium Botulinum. Authors: Schleberger, C. / Hochmann, H. / Barth, H. / 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 | 2j3x.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j3x.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 2j3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j3x_validation.pdf.gz | 460.8 KB | Display | wwPDB validaton report |
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Full document | 2j3x_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 2j3x_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2j3x_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3x ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3x | HTTPS FTP |
-Related structure data
Related structure data | 2j3vSC 2j3zC 2j42C 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: 49432.672 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: PET-3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O69275 | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 3 Details: PROTEIN: 10 MG/ML RESERVOIR: 0.1 M CITRAT PH 3.0, 0.8 M (NH4)2SO4 HANGING DROP 1:1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0332 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48 Å / Num. obs: 63100 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.75→1.82 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J3V Resolution: 1.75→47.14 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.834 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / 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: 20.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→47.14 Å
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Refine LS restraints |
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