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- PDB-2c8a: Structure of the wild-type C3bot1 Exoenzyme (Nicotinamide-bound s... -
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Open data
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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) | ||||||
![]() | MONO-ADP-RIBOSYLTRANSFERASE C3 | ||||||
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Function / homology | ![]() NAD+-protein ADP-ribosyltransferase activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.1 KB | Display | ![]() |
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PDB format | ![]() | 147.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c89C ![]() 2c8bC ![]() 2c8cC ![]() 2c8dC ![]() 2c8eC ![]() 2c8fC ![]() 1gzfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P15879, UniProt: Q7M0L1*PLUS, ![]() #2: Chemical | ChemComp-NCA / ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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