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- PDB-4qzd: Mouse Tdt, F405A mutant, in complex with a DSB substrate, C-C bas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qzd | ||||||
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Title | Mouse Tdt, F405A mutant, in complex with a DSB substrate, C-C base pair | ||||||
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![]() | TRANSFERASE/DNA / Terminal deoxynucleotidyltransferase / nucleus / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() 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 / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gouge, J. / Delarue, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.4 KB | Display | ![]() |
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PDB format | ![]() | 135 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qz8C ![]() 4qz9C ![]() 4qzaC ![]() 4qzbC ![]() 4qzcC ![]() 4qzeC ![]() 4qzfC ![]() 4qzgC ![]() 4qzhC ![]() 4qziC ![]() 4i2aS 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: 45627.914 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: F405A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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: 2094.394 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 67 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-DCT / | #7: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.49 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2012 / Details: Kirkpatrick-Baez pair of bi-morph mirrors |
Radiation | Monochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91501 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45 Å / Num. obs: 14140 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / Num. unique all: 1990 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4I2A Resolution: 2.7→43.56 Å / Cor.coef. Fo:Fc: 0.9369 / Cor.coef. Fo:Fc free: 0.9142 / SU R Cruickshank DPI: 0.69 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.666 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.307 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 83.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.455 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→43.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.92 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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