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Yorodumi- PDB-1r45: ADP-ribosyltransferase C3bot2 from Clostridium botulinum, triclin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r45 | ||||||
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Title | ADP-ribosyltransferase C3bot2 from Clostridium botulinum, triclinic form | ||||||
Components | Mono-ADP-ribosyltransferase C3 | ||||||
Keywords | TRANSFERASE / ADP-RIBOSYLTRANSFERASE / BINARY 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 phage c-st (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Gilliland, G.L. / Narumiya, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ADP-ribosyltransferase C3bot2 from Clostridium botulinum Authors: Teplyakov, A. / Obmolova, G. / Gilliland, G.L. / Narumiya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r45.cif.gz | 190 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r45.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 1r45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r45 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r45 | HTTPS FTP |
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-Related structure data
Related structure data | 1g24S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23225.521 Da / Num. of mol.: 4 / Fragment: mature protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium phage c-st (virus) / Strain: c003-9 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q00901, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Lithium Sulfate, 7% PEG 4000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 9, 1997 / Details: mirror |
Radiation | Monochromator: Germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→20 Å / Num. all: 118341 / Num. obs: 118341 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 12.4 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G24-A Resolution: 1.57→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.208 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083
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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: 18.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.608 Å / Total num. of bins used: 20 /
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