[English] 日本語
![](img/lk-miru.gif)
- PDB-4e7l: PFV integrase Strand Transfer Complex (STC-Mn*) following reactio... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4e7l | ||||||
---|---|---|---|---|---|---|---|
Title | PFV integrase Strand Transfer Complex (STC-Mn*) following reaction in crystallo, at 3.0 A resolution. | ||||||
![]() |
| ||||||
![]() | RECOMBINATION/DNA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 152.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 114 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4e7hC ![]() 4e7iC ![]() 4e7jC ![]() 4e7kC ![]() 3os0S 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, ![]() ![]() ![]() ![]() |
---|
-DNA chain , 4 types, 4 molecules CDtT
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others) |
---|---|
#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others) |
#4: DNA chain | Mass: 3977.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others) |
#5: DNA chain | Mass: 5204.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others) |
-Non-polymers , 3 types, 5 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
#6: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#7: Chemical | #8: Chemical | ChemComp-SO4 / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.54 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 34% PEG-400, 180MM LI2SO4,2.5MM EDTA, 100MM TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, 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![]() |
Reflection | Resolution: 3→40 Å / Num. obs: 32641 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3OS0 Resolution: 3.0001→37.947 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.179 Å2 / ksol: 0.308 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.0001→37.947 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|