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Yorodumi- PDB-2wn7: Structural Basis for Substrate Recognition in the Enzymatic Compo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wn7 | ||||||
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Title | Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile | ||||||
Components | ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT | ||||||
Keywords | TRANSFERASE / BINARY TOXIN / CDTA / ACTIN-ADPRT / RIBOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information transferase activity / nucleotide binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM DIFFICILE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Sundriyal, A. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Basis for Substrate Recognition in the Enzymatic Component of Adp-Ribosyltransferase Toxin Cdta from Clostridium Difficile. Authors: Sundriyal, A. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wn7.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wn7.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wn7_validation.pdf.gz | 778.1 KB | Display | wwPDB validaton report |
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Full document | 2wn7_full_validation.pdf.gz | 780.6 KB | Display | |
Data in XML | 2wn7_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 2wn7_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/2wn7 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wn7 | HTTPS FTP |
-Related structure data
Related structure data | 2wn4C 2wn5C 2wn6C 2wn8C 1giqS 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: 53323.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Plasmid: PMAL-P2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) CODON PLUS RIPL / References: UniProt: Q9KH42 |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.48 Å3/Da / Density % sol: 50.51 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.1M MIB BUFFER PH 9.0, 20% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 21369 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.85 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3 / % possible all: 74.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GIQ Resolution: 2.25→39.97 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.658 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.256 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.938 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.97 Å
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Refine LS restraints |
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