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Yorodumi- PDB-6go6: TdT chimera (Loop1 of pol mu) - ternary complex with downstream dsDNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6go6 | ||||||
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Title | TdT chimera (Loop1 of pol mu) - ternary complex with downstream dsDNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / NHEJ pathway / DNA bridging / DNA polymerase polX | ||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Loc'h, J. / Gerodimos, C.A. / Rosario, S. / Lieber, M.R. / Delarue, M. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6go6.cif.gz | 195.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6go6.ent.gz | 150.3 KB | Display | PDB format |
PDBx/mmJSON format | 6go6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6go6_validation.pdf.gz | 801.3 KB | Display | wwPDB validaton report |
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Full document | 6go6_full_validation.pdf.gz | 801.7 KB | Display | |
Data in XML | 6go6_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6go6_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/6go6 ftp://data.pdbj.org/pub/pdb/validation_reports/go/6go6 | HTTPS FTP |
-Related structure data
Related structure data | 6go3C 6go4C 6go5C 6go7C 1jmsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Dntt, Tdt, Polm, polmu / Production host: Escherichia coli (E. coli) References: UniProt: P09838, UniProt: Q9JIW4, DNA nucleotidylexotransferase, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 3 molecules GFE
#2: DNA chain | Mass: 2423.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 1810.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 332 molecules
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-DCT / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.12 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→47.46 Å / Num. obs: 45742 / % possible obs: 98.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 58.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.79 |
Reflection shell | Resolution: 2.09→2.22 Å / Rmerge(I) obs: 1.07 / Num. unique obs: 6958 / CC1/2: 0.612 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JMS Resolution: 2.09→47.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.137
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Displacement parameters | Biso mean: 61.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.09→47.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.14 Å / Total num. of bins used: 20
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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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