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- PDB-5twp: Pre-catalytic ternary complex of human Polymerase Mu with incomin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5twp | |||||||||||||||
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Title | Pre-catalytic ternary complex of human Polymerase Mu with incoming nonhydrolyzable UMPNPP | |||||||||||||||
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![]() | TRANSFERASE/DNA / Family X DNA polymerase / nonhomologous end-joining / DNA double strand break repair / ribonucleotide incorporation / 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 | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu. Authors: Moon, A.F. / Pryor, J.M. / 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 | ![]() | 177.1 KB | Display | ![]() |
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PDB format | ![]() | 132.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.9 KB | Display | ![]() |
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Full document | ![]() | 799.7 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5twqC ![]() 5twrC ![]() 5twsC ![]() 5vz7C ![]() 5vz8C ![]() 5vz9C ![]() 5vzaC ![]() 5vzbC ![]() 5vzcC ![]() 5vzdC ![]() 5vzeC ![]() 5vzfC ![]() 5vzgC ![]() 5vzhC ![]() 5vziC ![]() 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: 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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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 270 molecules ![](data/chem/img/2KH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-2KH / | ||||||
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#6: Chemical | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 95mM HEPES pH 7.5, 19% PEG4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 9, 2012 / 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: 2→50 Å / Num. obs: 31042 / % possible obs: 98.8 % / Redundancy: 6.1 % / Rsym value: 0.098 / Net I/σ(I): 14.37 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.71 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 2.001→21.143 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.61 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→21.143 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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