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Yorodumi- PDB-2wn6: Structural Basis for Substrate Recognition in the Enzymatic Compo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wn6 | ||||||
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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 / CDTA / ACTIN-ADPRT / BINARY TOXIN / 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: 1.96 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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Remark 700 | THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wn6.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wn6.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wn6_validation.pdf.gz | 829 KB | Display | wwPDB validaton report |
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Full document | 2wn6_full_validation.pdf.gz | 831.5 KB | Display | |
Data in XML | 2wn6_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 2wn6_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/2wn6 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wn6 | HTTPS FTP |
-Related structure data
Related structure data | 2wn4C 2wn5C 2wn7C 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: 53346.371 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 CODON PLUS RIPL DE3 / References: UniProt: Q9KH42 |
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#2: Chemical | ChemComp-NDP / |
#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: 2.4 Å3/Da / Density % sol: 48.86 % / 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 CCD / 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: 1.95→50 Å / Num. obs: 30820 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.18 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GIQ Resolution: 1.96→44.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.426 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.187 / 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: 31.859 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→44.28 Å
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Refine LS restraints |
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