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- PDB-3uob: Crystal structure of Human Thymine DNA Glycosylase Bound to Subst... -

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Basic information

Entry
Database: PDB / ID: 3uob
TitleCrystal structure of Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-deoxy-2'-beta-fluoro-cytidine
Components
  • 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3'
  • 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1FC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / dsDNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


G/U mismatch-specific uracil-DNA glycosylase activity / thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / DNA N-glycosylase activity / sodium ion binding ...G/U mismatch-specific uracil-DNA glycosylase activity / thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / DNA N-glycosylase activity / sodium ion binding / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / epigenetic regulation of gene expression / 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 / magnesium ion binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.011 Å
AuthorsZhang, L. / He, C.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA.
Authors: Zhang, L. / Lu, X. / Lu, J. / Liang, H. / Dai, Q. / Xu, G.L. / Luo, C. / Jiang, H. / He, C.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3'
D: 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1FC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'
A: G/T mismatch-specific thymine DNA glycosylase
B: G/T mismatch-specific thymine DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)59,7284
Polymers59,7284
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-35 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.418, 163.418, 54.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: DNA chain 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3'


Mass: 7121.597 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1FC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'


Mass: 7063.524 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein G/T mismatch-specific thymine DNA glycosylase / Thymine-DNA glycosylase / TDG


Mass: 22771.301 Da / Num. of mol.: 2 / Fragment: UNP residues 111-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Production host: Escherichia coli (E. coli) / References: UniProt: Q13569, thymine-DNA glycosylase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG3350, 0.2 M tripotassium citrate monohydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2011
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 11703 / Num. obs: 11703 / % possible obs: 59.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible all
3-3.054.10.53159.3
3.05-3.11163.3
3.11-3.17165.2
3.17-3.23169.8
3.23-3.28174.1
3.28-3.33175.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RBA

2rba


Resolution: 3.011→32.733 Å / SU ML: 0.99 / σ(F): 1.35 / Phase error: 32.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 596 10.03 %
Rwork0.2191 --
obs0.2247 11703 69.52 %
all-11703 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.407 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.0606 Å2-0 Å20 Å2
2---19.0606 Å2-0 Å2
3---38.1211 Å2
Refinement stepCycle: LAST / Resolution: 3.011→32.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 941 0 0 3764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013948
X-RAY DIFFRACTIONf_angle_d1.5235524
X-RAY DIFFRACTIONf_dihedral_angle_d24.0761548
X-RAY DIFFRACTIONf_chiral_restr0.144600
X-RAY DIFFRACTIONf_plane_restr0.007545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.011-3.14790.3566340.3225301X-RAY DIFFRACTION16
3.1479-3.31370.3427830.2961764X-RAY DIFFRACTION41
3.3137-3.52110.2911160.26411023X-RAY DIFFRACTION55
3.5211-3.79260.28881470.23841311X-RAY DIFFRACTION70
3.7926-4.17360.29771690.21731552X-RAY DIFFRACTION82
4.1736-4.77590.25342010.17991763X-RAY DIFFRACTION94
4.7759-6.01110.25812080.21871884X-RAY DIFFRACTION98
6.0111-32.73460.27632160.21791931X-RAY DIFFRACTION98

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