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Yorodumi- PDB-5wtz: Crystal structure of C. perfringens iota-like enterotoxin CPILE-a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wtz | ||||||
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Title | Crystal structure of C. perfringens iota-like enterotoxin CPILE-a with NAD+ | ||||||
Components | Binary enterotoxin of Clostridium perfringens component a | ||||||
Keywords | TOXIN / bacterial toxin / actin / CPILE-a / ADP-ribosylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å | ||||||
Authors | Toniti, W. / Yoshida, T. / Tsurumura, T. / Irikura, D. / Tsuge, H. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Crystal structure and structure-based mutagenesis of actin-specific ADP-ribosylating toxin CPILE-a as novel enterotoxin Authors: Toniti, W. / Yoshida, T. / Tsurumura, T. / Irikura, D. / Monma, C. / Kamata, Y. / Tsuge, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wtz.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wtz.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/5wtz ftp://data.pdbj.org/pub/pdb/validation_reports/wt/5wtz | HTTPS FTP |
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-Related structure data
Related structure data | 5gttSC 5wu0C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 47671.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: becA / Production host: Escherichia coli (E. coli) / References: UniProt: X5I2D7 |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Tris HCl, Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 38653 / % possible obs: 99.4 % / Redundancy: 6.3 % / Net I/σ(I): 12.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GTT Resolution: 1.803→47.606 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.803→47.606 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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