[English] 日本語
![](img/lk-miru.gif)
- PDB-4ed8: Human DNA polymerase eta - DNA ternary complex: Reaction in the T... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ed8 | ||||||
---|---|---|---|---|---|---|---|
Title | Human DNA polymerase eta - DNA ternary complex: Reaction in the TG crystal at pH 7.0, Normal translocation | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Zhao, Y. / Yang, W. | ||||||
![]() | ![]() Title: Watching DNA polymerase eta make a phosphodiester bond Authors: Nakamura, T. / Zhao, Y. / Yamagata, Y. / Hua, Y.J. / Yang, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 222.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 171.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 809.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 814.2 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ecqC ![]() 4ecrC ![]() 4ecsC ![]() 4ectC ![]() 4ecuC ![]() 4ecvC ![]() 4ecwC ![]() 4ecxC ![]() 4ecyC ![]() 4eczC ![]() 4ed0C ![]() 4ed1C ![]() 4ed2C ![]() 4ed3C ![]() 4ed6C ![]() 4ed7C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: Catalytic core (UNP RESIDUES 1-432) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#3: DNA chain | Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 485 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | #7: Chemical | ChemComp-DTP / | #8: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | CA A 503 AND MG A 504 ARE IN ALTERNATE CONFORMATI |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 0.1M MES, 6-17%(W/V) PEG 2K-MME, VAPOR DIFFUSION, temperature 293K, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 67307 / % possible obs: 96.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.631 / % possible all: 71.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.997 Å2 / ksol: 0.344 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.38 Å2 / Biso mean: 27.4114 Å2 / Biso min: 6.54 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.521→28.517 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|