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- PDB-6p1s: 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: 6p1s | ||||||
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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 AMP | ||||||
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![]() | TRANSFERASE/DNA / Family X polymerase / NHEJ / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
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 | ![]() | 191.2 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p1mC ![]() 6p1nC ![]() 6p1oC ![]() 6p1pC ![]() 6p1qC ![]() 6p1rC ![]() 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
-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: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 7 types, 343 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ATP / | ||||||||
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#6: Chemical | ChemComp-MN / | ||||||||
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-EPE / | #10: Chemical | ChemComp-EDO / | #11: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | The authors state that anomalous signal is observed for the metal A site (peak greater than 10 ...The authors state that anomalous signal is observed for the metal A site (peak greater than 10 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: 2.861 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% 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: Mar 27, 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: 1.75→50 Å / Num. obs: 46614 / % possible obs: 99.3 % / Redundancy: 12 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.06 / Rsym value: 0.06 / Χ2: 1.025 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.26 / Num. unique obs: 2182 / Rpim(I) all: 0.194 / Rrim(I) all: 0.568 / Rsym value: 0.452 / Χ2: 0.68 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.75→31.386 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→31.386 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.9262 Å / Origin y: -4.3784 Å / Origin z: -11.4618 Å
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Refinement TLS group | Selection details: all |