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Yorodumi- PDB-3oyd: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oyd | ||||||
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Title | Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI GS9160 | ||||||
Components |
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Keywords | RECOMBINATION / VIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / INHIBITOR / DNA-BINDING PROTEIN-DNA complex / VIRAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human spumaretrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å | ||||||
Authors | Hare, S. / Cherepanov, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Authors: Hare, S. / Vos, A.M. / Clayton, R.F. / Thuring, J.W. / Cummings, M.D. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oyd.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oyd.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 3oyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/3oyd ftp://data.pdbj.org/pub/pdb/validation_reports/oy/3oyd | HTTPS FTP |
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-Related structure data
Related structure data | 3oyaC 3oybSC 3oycC 3oyeC 3oyfC 3oygC 3oyhC 3oyiC 3oyjC 3oykC 3oylC 3oymC 3oynC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44456.695 Da / Num. of mol.: 2 / Fragment: UNP residues 752 to 1143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: POL / Plasmid: pSSH6P-PFV-INFL / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P14350 |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA non-transferred strand |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA transferred strand |
-Non-polymers , 7 types, 248 molecules
#4: Chemical | ChemComp-ZN / | ||||||||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-NH4 / | #8: Chemical | #9: Chemical | ChemComp-ZZV / | #10: 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: 3.93 Å3/Da / Density % sol: 68.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Jun 8, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→39.882 Å / Num. obs: 52902 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.108 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.01
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3OYB Resolution: 2.54→39.88 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.2112 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8348 / SU B: 7.401 / SU ML: 0.157 / SU R Cruickshank DPI: 0.2348 / SU Rfree: 0.1998 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.75 Å2 / Biso mean: 61.9538 Å2 / Biso min: 36.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→39.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.606 Å / Total num. of bins used: 20
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