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- PDB-5dqi: Crystal Structure of Human DNA Polymerase Eta Extending an O4-Eth... -
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Basic information
Entry | Database: PDB / ID: 5dqi | ||||||
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Title | Crystal Structure of Human DNA Polymerase Eta Extending an O4-Ethylthymidine : dA Pair By Inserting dCTP Opposite dG | ||||||
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![]() | Transferase/DNA / Catalytic Domain / DNA Damage / DNA-Directed DNA Polymerase / Adenosine Triphosphate / Y-family polymerase / trans-lesion synthesis (TLS) / DNA Binding / O4-Alkylthymidine / O4-Ethylthymidine / 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patra, A. / OFlaherty, D.K. / Egli, M. | ||||||
![]() | ![]() Title: Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta. Authors: O'Flaherty, D.K. / Patra, A. / Su, Y. / Guengerich, F.P. / Egli, M. / Wilds, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.9 KB | Display | ![]() |
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PDB format | ![]() | 85.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 811.7 KB | Display | ![]() |
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Full document | ![]() | 816.3 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dlfC ![]() 5dlgC ![]() 5dqgC ![]() 5dqhC ![]() 4o3nS 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: 3681.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2724.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 106 molecules ![](data/chem/img/DCP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DCP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M MES pH 5.5, 5mM Calcium chloride, 20% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2015 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 143943 / Num. obs: 20174 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 22.718 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.538 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4O3N Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.011 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.222 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→50 Å
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Refine LS restraints |
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