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- PDB-7cod: Post insertion complex of DNA polymerase Mu (K438A/Q441A) with 1-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cod | ||||||
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Title | Post insertion complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapped DNA | ||||||
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![]() | HYDROLASE/DNA / polymerase mu / misincorporation / gap filling / mutagenesis / HYDROLASE / HYDROLASE-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 | ![]() ![]() ![]() | ||||||
![]() | Guo, M. / Zhao, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of genome instability mediated by human DNA polymerase mu misincorporation. Authors: Guo, M. / Wang, Y. / Tang, Y. / Chen, Z. / Hou, J. / Dai, J. / Wang, Y. / Wang, L. / Xu, H. / Tian, B. / Hua, Y. / Zhao, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.2 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 793.6 KB | Display | ![]() |
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Full document | ![]() | 796.1 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7co6C ![]() 7co8C ![]() 7co9C ![]() 7coaC ![]() 7cobC ![]() 7cocC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53681.012 Da / Num. of mol.: 1 / Mutation: P410G, K438A, Q441A, deletion 398-409 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: 2731.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The 3' end dG (last one) is the product of polymerization reaction in crystal by soaking binary crystal with dGTP. The DNA sequence actually used for crystallization is CGTA. Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' phosphorylated dG / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 354 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / | ||||
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#6: Chemical | ChemComp-DGT / | ||||
#7: Chemical | #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 1,4-Dioxane, Tris-Hcl, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→29.773 Å / Num. obs: 41495 / % possible obs: 95.1 % / Redundancy: 4.701 % / Biso Wilson estimate: 25.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.04 / Χ2: 1.057 / Net I/σ(I): 24.19 / Num. measured all: 195058 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.8→29.773 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.28 / 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: 74.52 Å2 / Biso mean: 29.7598 Å2 / Biso min: 12.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→29.773 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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