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- PDB-7m8b: Human DNA Pol eta S113A with rA-ended primer and dATP: in crystal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m8b | ||||||
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Title | Human DNA Pol eta S113A with rA-ended primer and dATP: in crystallo reaction for 140 s | ||||||
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![]() | TRANSFERASE/DNA / DNA polymerase / Time resolved crystallography / deprotonation / DNA BINDING PROTEIN / 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 / damaged DNA binding / DNA-directed DNA polymerase / DNA replication / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gregory, M.T. / Gao, Y. / Yang, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction. Authors: Gregory, M.T. / Gao, Y. / Cui, Q. / 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 | ![]() | 136 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m7lC ![]() 7m7mC ![]() 7m7nC ![]() 7m7oC ![]() 7m7pC ![]() 7m7qC ![]() 7m7rC ![]() 7m7sC ![]() 7m7tC ![]() 7m7uC ![]() 7m7yC ![]() 7m7zC ![]() 7m80C ![]() 7m81C ![]() 7m82C ![]() 7m83C ![]() 7m84C ![]() 7m85C ![]() 7m86C ![]() 7m87C ![]() 7m88C ![]() 7m89C ![]() 7m8aC ![]() 7m8cC ![]() 7m8dC ![]() 4ecqS S: Starting model for refinement 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 / DNA chain / DNA/RNA hybrid , 3 types, 3 molecules ATP
#1: Protein | Mass: 48601.707 Da / Num. of mol.: 1 / Mutation: S113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3628.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: DNA/RNA hybrid | Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 6 types, 488 molecules 










#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | #7: Chemical | ChemComp-DTP / | #8: Chemical | ChemComp-DPO / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 6 / Details: 15% PEG 2000 MME, 100 mM MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→40 Å / Num. obs: 38394 / % possible obs: 98.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Χ2: 1.02 / Net I/σ(I): 10.9 / Num. measured all: 158226 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ecq Resolution: 1.85→31.46 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.15 Å2 / Biso mean: 27.6759 Å2 / Biso min: 5.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→31.46 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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