+Open data
-Basic information
Entry | Database: PDB / ID: 3os0 | ||||||
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Title | PFV strand transfer complex (STC) at 2.81 A resolution | ||||||
Components |
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Keywords | RECOMBINATION/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 / RECOMBINATION / RECOMBINATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / Resolution: 2.81 Å | ||||||
Authors | Maertens, G.N. / Hare, S. / Cherepanov, P. | ||||||
Citation | Journal: Nature / Year: 2010 Title: The mechanism of retroviral integration from X-ray structures of its key intermediates Authors: Maertens, G.N. / Hare, S. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3os0.cif.gz | 153.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3os0.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 3os0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3os0_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 3os0_full_validation.pdf.gz | 481.3 KB | Display | |
Data in XML | 3os0_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 3os0_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/3os0 ftp://data.pdbj.org/pub/pdb/validation_reports/os/3os0 | HTTPS FTP |
-Related structure data
Related structure data | 3os1C 3os2C 3l2qS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Strain: PFV / 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 , 4 types, 4 molecules CDtT
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
#4: DNA chain | Mass: 3977.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
#5: DNA chain | Mass: 5204.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
-Non-polymers , 3 types, 7 molecules
#6: Chemical | ChemComp-ZN / | ||
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#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS IS A NATURAL VARIATION. |
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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: 3.66 Å3/Da / Density % sol: 66.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 20% MPD, 40mM MgCl2, 50mM sodium cacodylate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→39.12 Å / Num. obs: 39563 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2.81→2.96 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 2 / Num. unique all: 5730 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L2Q Resolution: 2.81→39.12 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.886 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 61.061 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→39.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.883 Å / Total num. of bins used: 20
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