[English] 日本語
![](img/lk-miru.gif)
- PDB-4e7k: PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped pri... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4e7k | ||||||
---|---|---|---|---|---|---|---|
Title | PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution | ||||||
![]() |
| ||||||
![]() | 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 | ![]() 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 / host cell ...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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 | ![]() synthetic DNA (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maertens, G.N. / Cherepanov, P. | ||||||
![]() | ![]() Title: 3'-Processing and strand transfer catalysed by retroviral integrase in crystallo. Authors: Hare, S. / Maertens, G.N. / Cherepanov, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4e7hC ![]() 4e7iC ![]() 4e7jC ![]() 4e7lC ![]() 3os2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases |
---|
-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) |
---|---|
#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 ![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / | ||||||
---|---|---|---|---|---|---|---|
#6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.17 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.02→38.009 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|