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Yorodumi- PDB-4e7k: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped pri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e7k | ||||||
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Title | PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution | ||||||
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: 3.02 Å | ||||||
Authors | Maertens, G.N. / 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 | 4e7k.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e7k.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 4e7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/4e7k ftp://data.pdbj.org/pub/pdb/validation_reports/e7/4e7k | HTTPS FTP |
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-Related structure data
Related structure data | 4e7hC 4e7iC 4e7jC 4e7lC 3os2S 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 , 3 types, 3 molecules CDT
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: target DNA / Source: (synth.) synthetic DNA (others) |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: viral DNA / Source: (synth.) synthetic DNA (others) |
#4: DNA chain | Mass: 9226.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others) |
-Non-polymers , 5 types, 18 molecules
#5: Chemical | ChemComp-ZN / | ||||||
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#6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-PGE / | #9: 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: 3.99 Å3/Da / Density % sol: 69.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.4 Details: 34% PEG-400, 180MM LI2SO4,2.5MM EDTA, 100MM TRIS-HCL, pH 7.4, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→40 Å / Num. obs: 35032 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 3.02→3.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OS2 Resolution: 3.02→38.009 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 29.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.005 Å2 / ksol: 0.299 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.02→38.009 Å
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Refine LS restraints |
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LS refinement shell |
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