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Yorodumi- PDB-2c8f: Structure of the ARTT motif E214N mutant C3bot1 Exoenzyme (NAD-bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c8f | ||||||
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Title | Structure of the ARTT motif E214N mutant C3bot1 Exoenzyme (NAD-bound state, crystal form III) | ||||||
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: 2.5 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. 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 | 2c8f.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c8f.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 2c8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8f ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8f | HTTPS FTP |
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-Related structure data
Related structure data | 2c89C 2c8aC 2c8bC 2c8cC 2c8dC 2c8eC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23576.957 Da / Num. of mol.: 3 / Mutation: YES 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-NAD / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.8 % |
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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: ID14-3 / Wavelength: 0.933 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.88 Å / Num. obs: 22416 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZF Resolution: 2.5→29.88 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.878 / SU B: 13.831 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.885 / ESU R Free: 0.381 / 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: 46.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.88 Å
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Refine LS restraints |
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