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Yorodumi- PDB-3ki7: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ki7 | ||||||
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Title | Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-I | ||||||
Components | Cholix toxin | ||||||
Keywords | Transferase / toxin / ADP-ribosyl transferase / alpha-beta complex / diphthamide | ||||||
Function / homology | Function and homology information NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å | ||||||
Authors | Jorgensen, R. / Edwards, P.R. / Merrill, A.R. | ||||||
Citation | Journal: To be Published Title: Structure function analysis of soluble inhibitors of cholix toxin from Vibrio cholerae Authors: Jorgensen, R. / Edwards, P.R. / 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 | 3ki7.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ki7.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ki7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ki7_validation.pdf.gz | 714.3 KB | Display | wwPDB validaton report |
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Full document | 3ki7_full_validation.pdf.gz | 714.4 KB | Display | |
Data in XML | 3ki7_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3ki7_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/3ki7 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/3ki7 | HTTPS FTP |
-Related structure data
Related structure data | 3ki0C 3ki1C 3ki2C 3ki3C 3ki4C 3ki5C 3ki6C 2q6mS 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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-Components
#1: Protein | Mass: 23334.842 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 459-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: TP / Gene: chxa, toxA / Plasmid: pET28+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: Q5EK40, NAD+-diphthamide ADP-ribosyltransferase |
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#2: Chemical | ChemComp-G9I / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | COMPOUND G9I IS NAMED COMPOUND P5 IN THE PRIMARY CITATION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2008 |
Radiation | Monochromator: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 46297 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.121 / Χ2: 1.063 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4380 / Χ2: 0.809 / % possible all: 87.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q6M Resolution: 1.32→18.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.204 / SU ML: 0.024 / Isotropic thermal model: Isotropic with 10 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.051 / 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: 9.887 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→18.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.357 Å / Total num. of bins used: 20
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