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Yorodumi- PDB-4qzi: Mouse Tdt, F401A mutant, in complex with a DSB substrate and Zn2+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qzi | ||||||
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Title | Mouse Tdt, F401A mutant, in complex with a DSB substrate and Zn2+ | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Terminal deoxynucleotidyltransferase / nucleus / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Gouge, J. / Delarue, M. | ||||||
Citation | Journal: Embo J. / Year: 2015 Title: Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair. Authors: Gouge, J. / Rosario, S. / Romain, F. / Poitevin, F. / Beguin, P. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qzi.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qzi.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 4qzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/4qzi ftp://data.pdbj.org/pub/pdb/validation_reports/qz/4qzi | HTTPS FTP |
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-Related structure data
Related structure data | 4qz8C 4qz9C 4qzaC 4qzbC 4qzcC 4qzdC 4qzeC 4qzfC 4qzgC 4qzhC 4i2aS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45627.914 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: F401A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt / Production host: Escherichia coli (E. coli) / References: UniProt: P09838, DNA nucleotidylexotransferase |
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-DNA chain , 2 types, 3 molecules DUT
#2: DNA chain | Mass: 1810.258 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | | Mass: 2463.624 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 75 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-DCT / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | PROTEIN COMPRISES UNP RESIDUES 132-482 AND 503-530 WITH 483-502 DELETED. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12-17% PEG4000, 9-12% isopropanol, 100 mM sodium acetate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2012 |
Radiation | Monochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9725 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→45 Å / Num. obs: 13390 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 87.56 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1937 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4I2A Resolution: 2.65→22.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9487 / SU R Cruickshank DPI: 0.734 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.711 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.253 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 77.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.385 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→22.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.86 Å / Total num. of bins used: 7
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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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