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Yorodumi- PDB-4xzj: Crystal structure of ADP-ribosyltransferase Vis in complex with NAD -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xzj | ||||||
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Title | Crystal structure of ADP-ribosyltransferase Vis in complex with NAD | ||||||
Components | Putative 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pfoh, R. / Ravulapalli, R. / Merrill, A.R. / Pai, E.F. | ||||||
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 | 4xzj.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xzj.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/4xzj ftp://data.pdbj.org/pub/pdb/validation_reports/xz/4xzj | HTTPS FTP |
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-Related structure data
Related structure data | 4y1wSC 4yc0C 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 27037.045 Da / Num. of mol.: 1 / Fragment: residues 20-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio splendidus (bacteria) / Gene: V12B01_18061 / Plasmid: pet 28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A3UNN4, NAD+-protein-arginine ADP-ribosyltransferase |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 298 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 29, 2011 |
Radiation | Monochromator: multi-layer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 23562 / % possible obs: 94.7 % / Redundancy: 6.25 % / Rmerge(I) obs: 0.0445 / Net I/σ(I): 25.84 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.1799 / Mean I/σ(I) obs: 8.67 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y1W Resolution: 1.8→18.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2105 / WRfactor Rwork: 0.1802 / FOM work R set: 0.8824 / SU B: 4.226 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1222 / SU Rfree: 0.1147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.56 Å2 / Biso mean: 23.386 Å2 / Biso min: 13.86 Å2
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Refinement step | Cycle: final / Resolution: 1.8→18.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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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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