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- PDB-5jxy: Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jxy | ||||||
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Title | Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog | ||||||
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![]() | HYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / : / sodium ion binding / DNA N-glycosylase activity ...G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / : / sodium ion binding / DNA N-glycosylase activity / mismatched DNA binding / SUMO binding / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / chloride ion binding / regulation of embryonic development / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / protein kinase C binding / transcription coregulator activity / base-excision repair / PML body / : / double-stranded DNA binding / DNA-binding transcription factor binding / nucleic acid binding / damaged DNA binding / protein domain specific binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pidugu, L.S. / Pozharski, E. / Malik, S.S. / Drohat, A.C. | ||||||
![]() | ![]() Title: Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues. Authors: Coey, C.T. / Malik, S.S. / Pidugu, L.S. / Varney, K.M. / Pozharski, E. / Drohat, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ff8C ![]() 5hf7C ![]() 3ufjS 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
#1: Protein | Mass: 23070.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 8585.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium Chloride and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→19.7 Å / Biso Wilson estimate: 24.45 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UFJ Resolution: 1.71→19.7 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9229 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.108
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Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.272 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.75 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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