+Open data
-Basic information
Entry | Database: PDB / ID: 7pwj | ||||||
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Title | dUTPase from human in complex with Stl | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / dUTPase / dUTP / human / DNA | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / dTMP biosynthetic process / DNA replication / magnesium ion binding / mitochondrion ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / dTMP biosynthetic process / DNA replication / magnesium ion binding / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å | ||||||
Authors | Sanz-Frasquet, C. / Marina, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Microbiol Spectr / Year: 2023 Title: The Bacteriophage-Phage-Inducible Chromosomal Island Arms Race Designs an Interkingdom Inhibitor of dUTPases. Authors: Sanz-Frasquet, C. / Ciges-Tomas, J.R. / Alite, C. / Penades, J.R. / Marina, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pwj.cif.gz | 193 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pwj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pwj_validation.pdf.gz | 514.3 KB | Display | wwPDB validaton report |
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Full document | 7pwj_full_validation.pdf.gz | 525.3 KB | Display | |
Data in XML | 7pwj_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 7pwj_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/7pwj ftp://data.pdbj.org/pub/pdb/validation_reports/pw/7pwj | HTTPS FTP |
-Related structure data
Related structure data | 7pwxC 1q5uS 6h49S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules CCCEEEFFFAAABBBDDD
#1: Protein | Mass: 18100.340 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pETNKI-1.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F0J8 #2: Protein | Mass: 15910.923 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33316, dUTP diphosphatase |
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-Non-polymers , 4 types, 347 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.02 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6M ammonium sulphate and 1M lithium sulphate. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99186 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99186 Å / Relative weight: 1 |
Reflection | Resolution: 1.944→99.2 Å / Num. obs: 92354 / % possible obs: 98.48 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.944→1.995 Å / Num. unique obs: 5386 / CC1/2: 0.897 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H49, 1Q5U Resolution: 1.944→99.199 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.503 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.148 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.944→99.199 Å
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Refine LS restraints |
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LS refinement shell |
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