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- PDB-6p1q: 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: 6p1q | ||||||
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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 dCMP | ||||||
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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 | ![]() ![]() | ||||||
![]() | Pedersen, L.C. / Kaminski, A.M. / 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 | ![]() | 179.2 KB | Display | ![]() |
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PDB format | ![]() | 133.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.2 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p1mC ![]() 6p1nC ![]() 6p1oC ![]() 6p1pC ![]() 6p1rC ![]() 6p1sC ![]() 6p1tC ![]() 6p1uC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39844.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 2772.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 6 types, 326 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | #8: Chemical | ChemComp-PPV / | #9: Chemical | ChemComp-EPE / | #10: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | The authors state that weak anomalous signal is observed at two positions in this structure--at the ...The authors state that weak anomalous signal is observed at two positions in this structure--at the metal occupying the HhH2 site (peak greater than 5 sigma), and at the metal A site (peak greater than 4 sigma). No known anomalous scatterers were added to the crystallization or soaking solutions, so these positions have been putatively modeled as sodium and magnesium (respectively), which is consistent with their identities in other reported structures. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 100mM NaCl, 10% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 6, 2015 / 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: 1.9→50 Å / Num. obs: 36686 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Rsym value: 0.061 / Χ2: 1.124 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1768 / Rpim(I) all: 0.221 / Rrim(I) all: 0.486 / Rsym value: 0.43 / Χ2: 0.676 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.9→25.072 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25.072 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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