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Yorodumi- PDB-2c8a: Structure of the wild-type C3bot1 Exoenzyme (Nicotinamide-bound s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c8a | ||||||
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Title | Structure of the wild-type C3bot1 Exoenzyme (Nicotinamide-bound state, crystal form I) | ||||||
Components | MONO-ADP-RIBOSYLTRANSFERASE C3 | ||||||
Keywords | TRANSFERASE / C3 EXOENZYME / ARTT MOTIF / BACTERIAL TOXINS / GLYCOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / extracellular region Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM BOTULINUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Stura, E.A. / Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Structural Basis for the Nad-Hydrolysis Mechanism and the Artt-Loop Plasticity of C3 Exoenzymes. Authors: Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A. / Stura, E.A. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Nad Binding Induces Conformational Changes in Rho Adp-Ribosylating Clostridium Botulinum C3 Exoenzyme.J Authors: Menetrey, J. / Flatau, G. / Stura, E.A. / Charbonnier, J.B. / Gas, F. / Teulon, J.M. / Ledu, M.H. / Boquet, P. / Menez, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c8a.cif.gz | 184.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c8a.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 2c8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c8a_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 2c8a_full_validation.pdf.gz | 488.1 KB | Display | |
Data in XML | 2c8a_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 2c8a_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8a ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8a | HTTPS FTP |
-Related structure data
Related structure data | 2c89C 2c8bC 2c8cC 2c8dC 2c8eC 2c8fC 1gzfS 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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Unit cell |
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-Components
#1: Protein | Mass: 23591.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P15879, UniProt: Q7M0L1*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-NCA / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Details: 22.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9501 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9501 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→24.32 Å / Num. obs: 99953 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZF Resolution: 1.7→24.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.485 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→24.33 Å
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Refine LS restraints |
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