+Open data
-Basic information
Entry | Database: PDB / ID: 4e7h | ||||||
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Title | PFV intasome prior to 3'-processing, Apo form (UI-Apo) | ||||||
Components |
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Keywords | RECOMBINATION/DNA / protein-DNA complex / tetramer / HHCC motif / endonuclease / metal-binding / multifunctional enzyme / nuclease / nucleotidyltransferase / nucleus / transferase / virion / DNA-binding / zinc-binding / viral protein / recombination / viral protein-DNA complex / RECOMBINATION-DNA complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / 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 Synthetic DNA (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5701 Å | ||||||
Authors | Hare, S. / Cherepanov, P. | ||||||
Citation | Journal: Embo J. / Year: 2012 Title: 3'-Processing and strand transfer catalysed by retroviral integrase in crystallo. Authors: Hare, S. / Maertens, G.N. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e7h.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e7h.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/4e7h ftp://data.pdbj.org/pub/pdb/validation_reports/e7/4e7h | HTTPS FTP |
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-Related structure data
Related structure data | 4e7iC 4e7jC 4e7kC 4e7lC 3oy9S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44456.695 Da / Num. of mol.: 2 / Fragment: UNP Residues 752-1143 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, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases |
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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: viral DNA / Source: (synth.) Synthetic DNA (others) |
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#3: DNA chain | Mass: 5812.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others) |
-Non-polymers , 5 types, 248 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-HEZ / | #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
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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: 3.91 Å3/Da / Density % sol: 68.56 % |
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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, 2MM 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: Diamond / Beamline: I02 / Wavelength: 1.0389 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0389 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→40 Å / Num. obs: 50886 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OY9 Resolution: 2.5701→36.916 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 20.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.704 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5701→36.916 Å
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Refine LS restraints |
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LS refinement shell |
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