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- PDB-5kg3: Human DNA polymerase eta-DNA ternary complex: reaction first with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kg3 | ||||||
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Title | Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mM Mn2+ for 1800s then with 10 mM Mn2+ for 60s | ||||||
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![]() | replication / transferase/dna / in crystallo reaction / DNA polymerase / metal ion dependent catalysis / transferase-dna complex | ||||||
Function / homology | ![]() response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / 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 / error-free translesion synthesis / DNA synthesis involved in DNA repair / 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 | ![]() ![]() ![]() | ||||||
![]() | Gao, Y. / Yang, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Capture of a third Mg2+ is essential for catalyzing DNA synthesis. Authors: Gao, Y. / 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 | ![]() | 131.9 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kfaC ![]() 5kfbC ![]() 5kfcC ![]() 5kfdC ![]() 5kfeC ![]() 5kffC ![]() 5kfgC ![]() 5kfhC ![]() 5kfiC ![]() 5kfjC ![]() 5kfkC ![]() 5kflC ![]() 5kfmC ![]() 5kfnC ![]() 5kfoC ![]() 5kfpC ![]() 5kfqC ![]() 5kfrC ![]() 5kfsC ![]() 5kftC ![]() 5kfuC ![]() 5kfvC ![]() 5kfwC ![]() 5kfxC ![]() 5kfyC ![]() 5kfzC ![]() 5kg0C ![]() 5kg1C ![]() 5kg2C ![]() 5kg4C ![]() 5kg5C ![]() 5kg6C ![]() 5kg7C ![]() 5l9xC ![]() 4ecqS C: citing same article ( S: Starting model for refinement |
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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 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 / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 5 types, 473 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-DTP / | #7: Chemical | ChemComp-DPO / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6 / Details: 17% PEG 2000MME, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2014 / Details: 4*4 mosiac | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal-liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→20 Å / Num. obs: 49002 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 25.206 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Net I/σ(I): 14.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ECQ Resolution: 1.7→19.978 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 99.55 Å2 / Biso mean: 22.7138 Å2 / Biso min: 5.42 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→19.978 Å
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