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- PDB-3ufj: Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-fluoro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ufj | ||||||
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Title | Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-fluoro-2'-deoxyuridine | ||||||
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![]() | HYDROLASE/DNA / DNA damage / DNA repair / DNA binding / glycosidase / nucleus / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozharski, E. / Maiti, A. / Drohat, A.C. | ||||||
![]() | ![]() Title: Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Authors: Maiti, A. / Noon, M.S. / Mackerell, A.D. / 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 | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.2 KB | Display | ![]() |
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Full document | ![]() | 533.5 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 37.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rbaS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 23070.670 Da / Num. of mol.: 2 / Fragment: Core domain (UNP residues 111-308) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 7121.597 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 7020.500 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 20% PEG3350, 0.2 M potassium sodium tartrate tetrahydrate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2010 |
Radiation | Monochromator: side scattering I-beam bent single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.967→140.761 Å / Num. all: 17486 / Num. obs: 17456 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 102.2 Å2 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.967→3.04 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2RBA Resolution: 2.967→40.634 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / SU B: 38.948 / SU ML: 0.581 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.441 Å2
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Refinement step | Cycle: LAST / Resolution: 2.967→40.634 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.967→3.043 Å / Total num. of bins used: 20
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