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Open data
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Basic information
Entry | Database: PDB / ID: 5tyd | ||||||
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Title | DNA Polymerase Mu Reactant Complex, 10 mM Mg2+ (45 min) | ||||||
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![]() | Transferase/DNA / Time-Lapse Crystallography / Product Metal / DNA Polymerase Mu / Double Strand Break Repair / 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 | ![]() unidentified (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jamsen, J.A. / Wilson, S.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Authors: Jamsen, J.A. / Beard, W.A. / Pedersen, L.C. / Shock, D.D. / Moon, A.F. / Krahn, J.M. / Bebenek, K. / Kunkel, T.A. / Wilson, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.2 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.8 KB | Display | ![]() |
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Full document | ![]() | 837.3 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5txxC ![]() 5txzC ![]() 5tybC ![]() 5tycC ![]() 5tyeC ![]() 5tyfC ![]() 5tygC ![]() 5tyuC ![]() 5tyvC ![]() 5tywC ![]() 5tyxC ![]() 5tyyC ![]() 5tyzC ![]() 4m04S C: citing same article ( S: Starting model for refinement |
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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: 40054.434 Da / Num. of mol.: 1 / Fragment: UNP residues 132-494 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: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
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#3: DNA chain | Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
-Non-polymers , 8 types, 357 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-DTT / | #8: Chemical | ChemComp-TTP / | #9: Chemical | ChemComp-EPE / | #10: Chemical | ChemComp-EDO / #11: Chemical | ChemComp-PPV / | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 % / Mosaicity: 0.266 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 23, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.899→50 Å / Num. obs: 36696 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.08 Å2 / Rmerge(I) obs: 0.07 / Net I/av σ(I): 30 / Net I/σ(I): 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.899→34.941 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.01 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.04 Å2 / Biso mean: 22.759 Å2 / Biso min: 5.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.899→34.941 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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