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Yorodumi- PDB-2c8e: Structure of the ARTT motif E214N mutant C3bot1 Exoenzyme (Free s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c8e | ||||||
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Title | Structure of the ARTT motif E214N mutant C3bot1 Exoenzyme (Free 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: 1.6 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 | 2c8e.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c8e.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c8e_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 2c8e_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 2c8e_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 2c8e_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8e ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8e | HTTPS FTP |
-Related structure data
Related structure data | 2c89C 2c8aC 2c8bC 2c8cC 2c8dC 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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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-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN E, GLU 214 TO ASN ENGINEERED RESIDUE IN CHAIN F, GLU 214 TO ASN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 46.8 % |
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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 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.27 Å / Num. obs: 87212 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZF Resolution: 1.6→37.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.142 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / 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: 21.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→37.27 Å
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