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Open data
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Basic information
Entry | Database: PDB / ID: 4qz8 | ||||||
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Title | Mouse Tdt in complex with a DSB substrate, C-G 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 | ![]() | 179.2 KB | Display | ![]() |
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PDB format | ![]() | 138 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qz9C ![]() 4qzaC ![]() 4qzbC ![]() 4qzcC ![]() 4qzdC ![]() 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: 45704.008 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 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: 2134.418 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 92 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 | ChemComp-MG / |
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#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-DCT / |
#7: Water | ChemComp-HOH / |
-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: 2.52 Å3/Da / Density % sol: 51.22 % |
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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 2M-F / Detector: PIXEL / Date: Jul 30, 2012 Details: Pt-coated mirrors in a Kirkpatrick-Baez (KB) geometry |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.7 Å / Num. obs: 14082 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 91.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2042 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4I2A Resolution: 2.7→31.41 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.9126 / SU R Cruickshank DPI: 0.798 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.801 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.301 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 88.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→31.41 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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