+Open data
-Basic information
Entry | Database: PDB / ID: 4fk7 | ||||||
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Title | Crystal structure of Certhrax catalytic domain | ||||||
Components | Putative ADP-ribosyltransferase Certhrax | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / mono-ADP-ribosyltransferase / transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / metallopeptidase activity / toxin activity / nucleotide binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å | ||||||
Authors | Hong, B.S. / Dimov, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Certhrax Toxin, an Anthrax-related ADP-ribosyltransferase from Bacillus cereus. Authors: Visschedyk, D. / Rochon, A. / Tempel, W. / Dimov, S. / Park, H.W. / Merrill, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fk7.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fk7.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fk7_validation.pdf.gz | 729.8 KB | Display | wwPDB validaton report |
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Full document | 4fk7_full_validation.pdf.gz | 730.1 KB | Display | |
Data in XML | 4fk7_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4fk7_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/4fk7 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/4fk7 | HTTPS FTP |
-Related structure data
Related structure data | 4fxqC 4gf1C 3bw8S 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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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT HAS NOT BEEN DETERMINED |
-Components
#1: Protein | Mass: 26883.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE GENE TEMPLATE WAS PROVIDED BY PROF. A. ROD MERRILL (UNIVERSITY OF GUELPH) Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BCE_G9241_pBC218_0027 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q4MV79, Transferases; Glycosyltransferases; Pentosyltransferases | ||
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#2: Chemical | ChemComp-P34 / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | ChemComp-UNX / #5: 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: 2.11 Å3/Da / Density % sol: 41.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.4 Details: 2.9M ammonium sulfate, 0.1M bis-tris, pH 6.4, vapor diffusion, temperature 291K |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 12, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→35.92 Å / Num. obs: 21982 / % possible obs: 97.41 % / Redundancy: 7.05 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 60.2374 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3BW8 Resolution: 1.78→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 2.004 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. COOT and the molprobity server were also used during refinement
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.15 Å2 / Biso mean: 13.293 Å2 / Biso min: 4.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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