[English] 日本語
![](img/lk-miru.gif)
- PDB-5tws: Post-catalytic complex of human Polymerase Mu (H329A) with newly ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5tws | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Post-catalytic complex of human Polymerase Mu (H329A) with newly incorporated UTP | |||||||||||||||
![]() |
| |||||||||||||||
![]() | TRANSFERASE/DNA / Family X DNA polymerase / nonhomologous end-joining / DNA double strand break repair / ribonucleotide incorporation / TRANSFERASE-DNA complex | |||||||||||||||
Function / homology | ![]() Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu. Authors: Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 178.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.9 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5twpC ![]() 5twqC ![]() 5twrC ![]() 5vz7C ![]() 5vz8C ![]() 5vz9C ![]() 5vzaC ![]() 5vzbC ![]() 5vzcC ![]() 5vzdC ![]() 5vzeC ![]() 5vzfC ![]() 5vzgC ![]() 5vzhC ![]() 5vziC ![]() 4m04S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-DNA chain , 2 types, 2 molecules TD
#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / DNA/RNA hybrid , 2 types, 2 molecules AP
#1: Protein | Mass: 39777.094 Da / Num. of mol.: 1 Mutation: deletion of loop containing Pro398-Pro410, fused with glycine (labeled Gly410); H329A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#3: DNA/RNA hybrid | Mass: 1496.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 7 types, 338 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#6: Chemical | #7: Chemical | ChemComp-GOA / | #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-EDO / | #10: Chemical | ChemComp-EPE / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 62mM HEPES pH 7.5, 12.4% PEG4K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 17, 2016 / Details: Varimax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 39735 / % possible obs: 99.7 % / Redundancy: 8.4 % / Rsym value: 0.04 / Net I/σ(I): 45.3 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.96 / % possible all: 96.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.85→27.478 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 18.93
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→27.478 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|