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- PDB-5l1j: Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP O... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l1j | ||||||||||||
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Title | Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite O6-Methyl-2'-deoxyguanosine | ||||||||||||
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![]() | Transferase/DNA / Catalytic Domain / DNA Damage / DNA Polymerase / Lesion bypass / O6-Methyl-2'-deoxyguanosine / Y-family polymerase / translesion DNA synthesis (TLS) / DNA Binding protein. / 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. / Egli, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta. Authors: Patra, A. / Zhang, Q. / Guengerich, F.P. / Egli, M. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
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PDB format | ![]() | 93.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 812.7 KB | Display | ![]() |
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Full document | ![]() | 819.1 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l1iC ![]() 5l1kC ![]() 5l1lC ![]() 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: 3676.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 414 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1FZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1FZ.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-1FZ / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.77 % |
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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 Magnesium chloride, 16% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 33771 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 27.375 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.548 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4O3N Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.723 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.677 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→50 Å
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Refine LS restraints |
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