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- PDB-6d0m: Polymerase Eta post-insertion binary complex with cytarabine (AraC) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d0m | ||||||
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Title | Polymerase Eta post-insertion binary complex with cytarabine (AraC) | ||||||
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![]() | TRANSFERASE/DNA / Cytarabine / AraC / DNA damage / Translesion / DNA synthesis / DNA Replication / TRANSFERASE / 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 | ![]() ![]() ![]() | ||||||
![]() | Rechkoblit, O. / Aggarwal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for polymerase eta-promoted resistance to the anticancer nucleoside analog cytarabine. Authors: Rechkoblit, O. / Choudhury, J.R. / Buku, A. / Prakash, L. / Prakash, S. / Aggarwal, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.6 KB | Display | ![]() |
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PDB format | ![]() | 159.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 459.6 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d0zC ![]() 4j9pS 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
#1: Protein | Mass: 48645.762 Da / Num. of mol.: 1 / Fragment: residues 1-432 / Mutation: C406M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Engineered / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2731.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Engineered / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES buffer, PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Oct 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→45 Å / Num. obs: 39467 / % possible obs: 99.7 % / Redundancy: 12 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1849 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J9P Resolution: 1.832→42.68 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.832→42.68 Å
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Refine LS restraints |
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LS refinement shell |
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