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- PDB-4dl6: Human DNA polymerase eta extending primer immediately after cispl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dl6 | ||||||
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Title | Human DNA polymerase eta extending primer immediately after cisplatin crosslink (Pt-GG3). | ||||||
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![]() | TRANSFERASE/DNA/INHIBITOR / cisplatin / chemoresistence / translesion synthesis / human DNA polymerse eta / kinetics / molecular splint / inhibition / DNA distorsion / second TLS polymerase / nucleotidyl transfer reaction / PCNA / TRANSFERASE-DNA-INHIBITOR 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 / regulation of DNA repair / error-prone translesion synthesis / 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 / regulation of DNA repair / error-prone translesion synthesis / 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 | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Biertumpfel, C. / Gregory, M. / Hua, Y. / Hanaoka, F. / Yang, W. | ||||||
![]() | ![]() Title: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Authors: Zhao, Y. / Biertumpfel, C. / Gregory, M.T. / Hua, Y.J. / Hanaoka, F. / Yang, W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 795.2 KB | Display | ![]() |
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Full document | ![]() | 809.4 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dl2C ![]() 4dl3C ![]() 4dl4C ![]() 4dl5C ![]() 4dl7C ![]() 3mr2S 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 , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: hPolh 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: 3622.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cisplatin-crosslinked oligonucleotide, chain T |
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#3: DNA chain | Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide, chain P |
-Non-polymers , 4 types, 63 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/XG4.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/XG4.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-XG4 / | #6: Chemical | ChemComp-CPT / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % |
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Crystal grow | Temperature: 293 K / pH: 6 Details: MES, MgCl2, PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2010 Details: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING |
Radiation | Monochromator: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.05 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 15481 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.239 / Rsym value: 0.116 / Net I/σ(I): 7.25 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.87 / Rsym value: 0.676 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3MR2 Resolution: 2.5→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 1.35 / Phase error: 27.34 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.31 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell |
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