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Open data
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Basic information
Entry | Database: PDB / ID: 5tyz | |||||||||
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Title | DNA Polymerase Mu Product Complex, Mn2+ (960 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 | ![]() | 195.1 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.8 KB | Display | ![]() |
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Full document | ![]() | 486.3 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5txxC ![]() 5txzC ![]() 5tybC ![]() 5tycC ![]() 5tydC ![]() 5tyeC ![]() 5tyfC ![]() 5tygC ![]() 5tyuC ![]() 5tyvC ![]() 5tywC ![]() 5tyxC ![]() 5tyyC ![]() 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 , 7 types, 326 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MN / #6: Chemical | ChemComp-NA / | #7: Chemical | #8: Chemical | ChemComp-EPE / | #9: Chemical | #10: Chemical | ChemComp-GOA / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % / Mosaicity: 0.665 ° |
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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: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 11, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 32271 / % possible obs: 99.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 23.77 Å2 / Rmerge(I) obs: 0.095 / Χ2: 1.217 / Net I/av σ(I): 22.237 / Net I/σ(I): 8.5 / Num. measured all: 272826 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.977→21.982 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.22 / 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: 96.31 Å2 / Biso mean: 36.3937 Å2 / Biso min: 18.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.977→21.982 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: 11
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Refinement TLS params. | Method: refined / Origin x: 2.9425 Å / Origin y: -4.4109 Å / Origin z: -11.6661 Å
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Refinement TLS group |
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