+Open data
-Basic information
Entry | Database: PDB / ID: 4y1w | ||||||
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Title | Vis toxin, an ADP-ribosyltransferase from Vibrio Splendidus | ||||||
Components | NAD(+)--arginine ADP-ribosyltransferase Vis | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / nucleotide binding / extracellular region Similarity search - Function | ||||||
Biological species | Vibrio splendidus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ravulapalli, R. / Tempel, W. / Merrrill, A.R. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Characterization of Vis Toxin, a Novel ADP-Ribosyltransferase from Vibrio splendidus. Authors: Ravulapalli, R. / Lugo, M.R. / Pfoh, R. / Visschedyk, D. / Poole, A. / Fieldhouse, R.J. / Pai, E.F. / 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 | 4y1w.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y1w.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 4y1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/4y1w ftp://data.pdbj.org/pub/pdb/validation_reports/y1/4y1w | HTTPS FTP |
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-Related 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: 27037.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio splendidus (bacteria) / Gene: V12B01_18061 / Production host: Escherichia coli (E. coli) References: UniProt: A3UNN4, NAD+-protein-arginine ADP-ribosyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Jeffamine ED-2001, 0.1 M Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→35.404 Å / Num. obs: 50597 / % possible obs: 97.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.0639 / Net I/σ(I): 14.73 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 83.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.404 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 17.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→35.404 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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