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Open data
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Basic information
Entry | Database: PDB / ID: 6go7 | ||||||
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Title | TdT chimera (Loop1 of pol mu) - full DNA synapsis complex | ||||||
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![]() | DNA BINDING PROTEIN / NHEJ pathway / DNA bridging / DNA polymerase polX | ||||||
Function / homology | ![]() DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loc'h, J. / Gerodimos, C.A. / Rosario, S. / Lieber, M.R. / Delarue, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction. Authors: Loc'h, J. / Gerodimos, C.A. / Rosario, S. / Tekpinar, M. / Lieber, M.R. / Delarue, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.8 KB | Display | ![]() |
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PDB format | ![]() | 148.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800 KB | Display | ![]() |
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Full document | ![]() | 804.3 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6go3C ![]() 6go4C ![]() 6go5C ![]() 6go6C ![]() 1jmsS 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: 45848.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol ...Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P09838, UniProt: Q9JIW4, DNA nucleotidylexotransferase, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 6 molecules FGEHIJ
#2: DNA chain | Mass: 1810.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 2094.394 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 183 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-DCT / |
#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 19-25% PEG 4000, 100-400 mM lithium sulfate, 100 mM tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8728 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→44.99 Å / Num. obs: 16488 / % possible obs: 94.7 % / Redundancy: 2 % / Biso Wilson estimate: 60.47 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.135 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.55→2.7 Å / Rmerge(I) obs: 0.762 / Num. unique obs: 2605 / CC1/2: 0.554 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JMS Resolution: 2.55→44.99 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.877 / SU R Cruickshank DPI: 0.689 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.795 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.269
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Displacement parameters | Biso mean: 49.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.55→44.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.73 Å / Total num. of bins used: 8
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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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