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Yorodumi- PDB-3zez: Phage dUTPases control transfer of virulence genes by a proto- on... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zez | ||||||
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Title | Phage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism.(Staphylococcus bacteriophage 80alpha dUTPase with dUPNHPP). | ||||||
Components | DUTPASE | ||||||
Keywords | HYDROLASE / STAPHYLOCOCCUS AUREUS / PHAGE / PATHOGENICITY ISLAND / SAPI INDUCTION / GENE TRANSFER / MOONLIGHTING PROTEINS / DUTPASE / DUTP / G-PROTEIN / P-LOOP | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS PHAGE 80ALPHA (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tormo-Mas, M.A. / Donderis, J. / Garcia-Caballer, M. / Alt, A. / Mir-Sanchis, I. / Marina, A. / Penades, J.R. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Phage Dutpases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-Like Mechanism. Authors: Tormo-Mas, M.A. / Donderis, J. / Garcia-Caballer, M. / Alt, A. / Mir-Sanchis, I. / Marina, A. / Penades, J.R. #1: Journal: Nature / Year: 2010 Title: Moonlighting Bacteriophage Proteins Derepress Staphylococcal Pathogenicity Islands. Authors: Tormo-Mas, M.A. / Mir, I. / Shrestha, A. / Tallent, S.M. / Campoy, S. / Lasa, I. / Barbe, J. / Novick, R.P. / Christie, G.E. / Penades, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zez.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zez.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zez_validation.pdf.gz | 812.8 KB | Display | wwPDB validaton report |
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Full document | 3zez_full_validation.pdf.gz | 813.1 KB | Display | |
Data in XML | 3zez_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 3zez_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3zez ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3zez | HTTPS FTP |
-Related structure data
Related structure data | 3zf0C 3zf1C 3zf2C 3zf3C 3zf4C 3zf5C 3zf6C 2hquS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22667.627 Da / Num. of mol.: 1 / Fragment: TRIMERIC DUTPASE Source method: isolated from a genetically manipulated source Details: STRUCTURE IN PRESENCE OF DUPNHPP AND MAGNESIUM / Source: (gene. exp.) STAPHYLOCOCCUS PHAGE 80ALPHA (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ZF98, dUTP diphosphatase |
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-Non-polymers , 5 types, 69 molecules
#2: Chemical | #3: Chemical | ChemComp-DUP / | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE |
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Crystal grow | Details: 2-6% TERT-BUTANOL, 0.1M TRIS (PH 8.5), 30-50% MPD OR PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44.33 Å / Num. obs: 5949 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HQU Resolution: 2.8→39.65 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAINS WITH NO ELECTRON DENSITY ARE REFINED WITH 0 OCCUANCY
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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: 50.523 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→39.65 Å
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