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Yorodumi- PDB-1gzf: Structure of the Clostridium botulinum C3 exoenzyme (wild-type) i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gzf | ||||||
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Title | Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD | ||||||
Components | MONO-ADP-RIBOSYLTRANSFERASE C3 | ||||||
Keywords | TRANSFERASE / ADP-RIBOSYLTRANSFERASE / BACTERIAL TOXIN / C3 EXOENZYME | ||||||
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 / OTHER / Resolution: 1.95 Å | ||||||
Authors | Menetrey, J. / Flatau, G. / Stura, E.A. / Charbonnier, J.B. / Gas, F. / Teulon, J.M. / Le Du, M.H. / Boquet, P. / Menez, A. | ||||||
Citation | 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. / Le Du, 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 | 1gzf.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzf.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzf ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzf | HTTPS FTP |
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-Related structure data
-Links
-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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23591.969 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 41-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P15879, Transferases; Glycosyltransferases; Pentosyltransferases |
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-Non-polymers , 5 types, 577 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NIR / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 41.5 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3 Details: 22.5 % PEG 3350 W/W, 100MM LI2SO4, 80 MM ACID CITRIC PH 3 ADDED WITH 20MM NAD FOR 60MN | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 3 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.009 |
Detector | Date: Mar 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 62950 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 157546 |
Reflection shell | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 2 Å / % possible obs: 96.2 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.95→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: DISORDERED N- AND C-TERMINII WERE NOT MODELED
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |