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- PDB-4ecq: Human DNA polymerase eta- DNA ternary complex: AT crystal at pH6.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ecq | ||||||
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Title | Human DNA polymerase eta- DNA ternary complex: AT crystal at pH6.8(K+ MES) with 1 Ca2+ ion | ||||||
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![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.3 KB | Display | ![]() |
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PDB format | ![]() | 174.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.8 KB | Display | ![]() |
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Full document | ![]() | 805.2 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ecrC ![]() 4ecsC ![]() 4ectC ![]() 4ecuC ![]() 4ecvC ![]() 4ecwC ![]() 4ecxC ![]() 4ecyC ![]() 4eczC ![]() 4ed0C ![]() 4ed1C ![]() 4ed2C ![]() 4ed3C ![]() 4ed6C ![]() 4ed7C ![]() 4ed8C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 449 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / | ||||
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#5: Chemical | #6: Chemical | ChemComp-DTP / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, 6-17%(W/V) PEG 2K-MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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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: 1.5→50 Å / Num. obs: 72821 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.98 Å2 / Rsym value: 0.058 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.618 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.637 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.67 Å2 / Biso mean: 27.27 Å2 / Biso min: 4.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→24.012 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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