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- PDB-3zf5: Phage dUTPases control transfer of virulence genes by a proto-onc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zf5 | ||||||
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Title | Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y84F mutant with dUpNHpp). | ||||||
![]() | DUTPASE | ||||||
![]() | HYDROLASE / PATHOGENICITY ISLAND / SAPI INDUCTION / GENE TRANSFER / MOONLIGHTING PROTEINS / G-PROTEIN / P-LOOP | ||||||
Function / homology | ![]() dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tormo-Mas, M.A. / Donderis, J. / Garcia-Caballer, M. / Alt, A. / Mir-Sanchis, I. / Marina, A. / Penades, J.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.2 KB | Display | ![]() |
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PDB format | ![]() | 34 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.9 KB | Display | ![]() |
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Full document | ![]() | 789.1 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zezSC ![]() 3zf0C ![]() 3zf1C ![]() 3zf2C ![]() 3zf3C ![]() 3zf4C ![]() 3zf6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 22651.627 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: STRUCTURE IN PRESENCE OF DUMP / Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-DUP / | ||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.75 % / Description: NONE |
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Crystal grow | Details: 2-8% TERT-BUTANOL, 0.1M TRIS (PH 8.5), 30-50% MPD PR PEG400. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→14.9 Å / Num. obs: 4719 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 0.35 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZEZ Resolution: 3.2→14.71 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.807 / SU B: 15.769 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL MET IS NOT TRACED. RESIDUES F115, K117, E118 AND E159 ARE TRACED AS A BECAUSE OF LACK OF ELECTRON DENSITY.
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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: 29.684 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→14.71 Å
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Refine LS restraints |
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