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Yorodumi- PDB-3ki0: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ki0 | ||||||
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Title | Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-D | ||||||
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 / Resolution: 1.29 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 | 3ki0.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ki0.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ki0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ki0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3ki0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ki0_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3ki0_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/3ki0 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/3ki0 | HTTPS FTP |
-Related structure data
Related structure data | 3ki1C 3ki2C 3ki3C 3ki4C 3ki5C 3ki6C 3ki7C 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 | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Nonpolymer details | COMPOUND G9D IS NAMED COMPOUND P1 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: 2.19 Å3/Da / Density % sol: 43.96 % |
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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: 1.29→40 Å / Num. obs: 51669 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 20.179 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.54 |
Reflection shell | Resolution: 1.29→1.42 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 77737 / Num. unique all: 11984 / Num. unique obs: 11984 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q6M Resolution: 1.29→19.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.888 / SU B: 1.753 / SU ML: 0.033 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.054 / 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 max: 56.01 Å2 / Biso mean: 19.21 Å2 / Biso min: 7.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→19.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.29→1.325 Å / Total num. of bins used: 20
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