[English] 日本語
![](img/lk-miru.gif)
- PDB-4ed0: Human DNA polymerase eta - DNA ternary complex: AT crystal at pH ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ed0 | ||||||
---|---|---|---|---|---|---|---|
Title | Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.8 (Na+ MES) with 1 Ca2+ ion | ||||||
![]() |
| ||||||
![]() | 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 | ![]() | 129.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 801.4 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ecqC ![]() 4ecrC ![]() 4ecsC ![]() 4ectC ![]() 4ecuC ![]() 4ecvC ![]() 4ecwC ![]() 4ecxC ![]() 4ecyC ![]() 4eczC ![]() 4ed1C ![]() 4ed2C ![]() 4ed3C ![]() 4ed6C ![]() 4ed7C ![]() 4ed8C 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: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#3: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 556 molecules ![](data/chem/img/NA.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 | ChemComp-NA / | ||||
---|---|---|---|---|---|
#5: Chemical | ChemComp-CA / | ||||
#6: Chemical | #7: Chemical | ChemComp-DTP / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | GLU A 116 HAS THE FOLLOWING ALTERNATE CONFIGURATION. ALTERNATE A HAS GLU 116 (OCCUPANCY 0.40), ...GLU A 116 HAS THE FOLLOWING ALTERNATE CONFIGURAT |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, 6-17%(W/V) PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 54218 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rsym value: 0.068 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.433 / % possible all: 92 |
-
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: 36.811 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.81 Å2 / Biso mean: 21.2084 Å2 / Biso min: 4.03 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.653→28.517 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|