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- PDB-5vzi: Post-catalytic complex of human Polymerase Mu (W434H) mutant with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vzi | |||||||||||||||
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Title | Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming dTTP | |||||||||||||||
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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 | ![]() | 189.2 KB | Display | ![]() |
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PDB format | ![]() | 142.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5twpC ![]() 5twqC ![]() 5twrC ![]() 5twsC ![]() 5vz7C ![]() 5vz8C ![]() 5vz9C ![]() 5vzaC ![]() 5vzbC ![]() 5vzcC ![]() 5vzdC ![]() 5vzeC ![]() 5vzfC ![]() 5vzgC ![]() 5vzhC ![]() 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: 39796.094 Da / Num. of mol.: 1 / Fragment: UNP residues 134-494 Mutation: W434H, deletion of Pro398-Pro410 replaced by Gly410 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: 1495.023 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, 455 molecules ![](data/chem/img/TTP.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 | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | Anomalous signal is observed at one position in this structure at the metal occupying the HhH2 site ...Anomalous signal is observed at one position in this structure at the metal occupying the HhH2 site (peak greater than 10 sigma). No known anomalous scatterers were added, so this position has been putatively modeled as sodium, which is consistent with its identity in other reported structures. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 95mM HEPES, 19% PEG4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2017 / Details: Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 73085 / % possible obs: 97.9 % / Redundancy: 7 % / Rpim(I) all: 0.024 / Rsym value: 0.058 / Χ2: 0.931 / Net I/σ(I): 26.72 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 3020 / CC1/2: 0.833 / Rpim(I) all: 0.249 / Rsym value: 0.517 / Χ2: 0.772 / % possible all: 82.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.5→32.875 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 17.67 / 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: 1.5→32.875 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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