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Yorodumi- PDB-3zf5: Phage dUTPases control transfer of virulence genes by a proto-onc... -
+Open data
-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). | ||||||
Components | DUTPASEDUTP diphosphatase | ||||||
Keywords | HYDROLASE / PATHOGENICITY ISLAND / SAPI INDUCTION / GENE TRANSFER / MOONLIGHTING PROTEINS / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 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 | 3zf5.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zf5.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 3zf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/3zf5 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/3zf5 | HTTPS FTP |
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-Related structure data
Related structure data | 3zezSC 3zf0C 3zf1C 3zf2C 3zf3C 3zf4C 3zf6C 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 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.) STAPHYLOCOCCUS PHAGE 80ALPHA (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ZF98, dUTP diphosphatase | ||||
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#2: Chemical | ChemComp-DUP / | ||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: ROTATING ANODE / Wavelength: 1.54 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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