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Yorodumi- PDB-4e7j: PFV integrase Target Capture Complex, Apo form (TCC-Apo), at 3.15... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e7j | ||||||
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Title | PFV integrase Target Capture Complex, Apo form (TCC-Apo), at 3.15 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 / DNA integration / virion component / 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 / host cell ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / aspartic-type endopeptidase activity / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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: 3.1501 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. #1: Journal: To be Published Title: 3'-Processing and strand transfer calalysed by retroviral integrase in crystallo 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 | 4e7j.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e7j.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e7j_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 4e7j_full_validation.pdf.gz | 486.6 KB | Display | |
Data in XML | 4e7j_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 4e7j_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/4e7j ftp://data.pdbj.org/pub/pdb/validation_reports/e7/4e7j | HTTPS FTP |
-Related structure data
Related structure data | 4e7hC 4e7iC 4e7kC 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: synthetic DNA |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA |
#4: DNA chain | Mass: 9226.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA |
-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-ZN / |
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#6: Chemical | ChemComp-SO4 / |
-Details
Sequence details | THIS IS A NATURAL VARIANT. |
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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: 3.7 Å3/Da / Density % sol: 66.74 % |
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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: 3.15→40 Å / Num. obs: 28471 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.15→3.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OS2 Resolution: 3.1501→36.976 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 26.99 / 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: 51.867 Å2 / ksol: 0.317 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1501→36.976 Å
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Refine LS restraints |
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LS refinement shell |
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