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Yorodumi- PDB-5h03: Crystal structure of an ADP-ribosylating toxin BECa from C. perfr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h03 | ||||||
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Title | Crystal structure of an ADP-ribosylating toxin BECa from C. perfringens | ||||||
Components | Binary enterotoxin of Clostridium perfringens component a | ||||||
Keywords | TOXIN / ADP-ribosyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Kawahara, K. / Yonogi, S. / Munetomo, R. / Oki, H. / Yoshida, T. / Ohkubo, T. / Kumeda, Y. / Matsuda, S. / Kodama, T. / Iida, T. / Nakamura, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Authors: Kawahara, K. / Yonogi, S. / Munetomo, R. / Oki, H. / Yoshida, T. / Kumeda, Y. / Matsuda, S. / Kodama, T. / Ohkubo, T. / Iida, T. / Nakamura, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h03.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h03.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 5h03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/5h03 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/5h03 | HTTPS FTP |
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-Related structure data
Related structure data | 5h04C 1girS 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
#1: Protein | Mass: 47527.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: OS1 / Gene: becA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X5I2D7 |
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#2: 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: 2.1 Å3/Da / Density % sol: 41.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 100 mM Tris-HC, 450 mM magunesium chloride, 23% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 5, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.89→37.12 Å / Num. obs: 31752 / % possible obs: 98.4 % / Redundancy: 9.54 % / Biso Wilson estimate: 24.47 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gir Resolution: 1.89→37.123 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.75 Å2 / Biso mean: 30.6086 Å2 / Biso min: 8.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→37.123 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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