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- PDB-6p1u: Post-catalytic nicked complex of human DNA Polymerase Mu with 1-n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p1u | ||||||
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Title | Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated CMP | ||||||
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![]() | TRANSFERASE / Family X polymerase / NHEJ | ||||||
Function / homology | ![]() Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kaminski, A.M. / Pedersen, L.C. / Bebenek, K. / Chiruvella, K.K. / Ramsden, D.A. / Kunkel, T.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine. Authors: Kaminski, A.M. / Chiruvella, K.K. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184 KB | Display | ![]() |
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PDB format | ![]() | 136.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 815.6 KB | Display | ![]() |
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Full document | ![]() | 817 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p1mC ![]() 6p1nC ![]() 6p1oC ![]() 6p1pC ![]() 6p1qC ![]() 6p1rC ![]() 6p1sC ![]() 6p1tC ![]() 6p1vC ![]() 6p1wC ![]() 4m04S 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
-DNA chain , 2 types, 2 molecules TD
#2: DNA chain | Mass: 2772.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein / DNA/RNA hybrid , 2 types, 2 molecules AP
#1: Protein | Mass: 39844.160 Da / Num. of mol.: 1 / Fragment: residues 134-494 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: DNA/RNA hybrid | Mass: 1496.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 8 types, 314 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/CTP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/CTP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MN / | ||||||||||||
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#6: Chemical | #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-PPV / | #9: Chemical | ChemComp-CTP / | #10: Chemical | ChemComp-EPE / | #11: Chemical | ChemComp-EDO / | #12: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | The authors state that anomalous signal is observed for the metal A site (peak greater than 6 sigma) ...The authors state that anomalous signal is observed for the metal A site (peak greater than 6 sigma), though no anomalous scatterers were added to the crystallization or soaking solutions. Therefore, this metal has been modeled as manganese, based on the coordination geometry and interatomic distances. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 94mM HEPES pH 7.5, 94mM NaCl, 9.4% v/s PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 13, 2017 / Details: VARIMAX HF |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 46921 / % possible obs: 100 % / Redundancy: 8.3 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Rsym value: 0.063 / Χ2: 1.014 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.84 / Num. unique obs: 2265 / CC1/2: 0.833 / Rpim(I) all: 0.27 / Rrim(I) all: 0.623 / Rsym value: 0.56 / Χ2: 1.035 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.75→34.982 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→34.982 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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