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- PDB-3uo7: Crystal structure of Human Thymine DNA Glycosylase Bound to Subst... -

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Basic information

Entry
Database: PDB / ID: 3uo7
TitleCrystal structure of Human Thymine DNA Glycosylase Bound to Substrate 5-carboxylcytosine
Components
  • 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*AP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3'
  • 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1CC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / dsDNA with 5caC / HYDROLASE-DNA complex
Function / homology
Function and homology information


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 / SUMO binding ...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 / SUMO binding / mismatched DNA 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 / damaged DNA binding / nucleic acid 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: 3.002 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*AP*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*(1CC)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)59,6084
Polymers59,6084
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-36 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.352, 164.352, 57.569
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*AP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3'


Mass: 7105.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1CC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'


Mass: 7045.534 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein G/T mismatch-specific thymine DNA glycosylase / Thymine-DNA glycosylase / TDG


Mass: 22728.275 Da / Num. of mol.: 2 / Fragment: UNP residues 111-308 / Mutation: N140A
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: 3.77 Å3/Da / Density % sol: 67.33 %
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: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 14639 / Num. obs: 14639 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible all
3-3.053.60.73199.9
3.05-3.111100
3.11-3.171100
3.17-3.231100
3.23-3.281100
3.28-3.331100

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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 2BRA

2bra


Resolution: 3.002→36.613 Å / SU ML: 0.88 / σ(F): 1.35 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 731 9.95 %RANDOM
Rwork0.2267 ---
obs0.232 14639 81.23 %-
all-14639 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.461 Å2 / ksol: 0.285 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.4135 Å2-0 Å20 Å2
2---7.4135 Å2-0 Å2
3---14.827 Å2
Refinement stepCycle: LAST / Resolution: 3.002→36.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 938 0 0 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013956
X-RAY DIFFRACTIONf_angle_d1.4285533
X-RAY DIFFRACTIONf_dihedral_angle_d25.3151551
X-RAY DIFFRACTIONf_chiral_restr0.134601
X-RAY DIFFRACTIONf_plane_restr0.007547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.002-3.10960.3226300.4265254X-RAY DIFFRACTION16
3.1096-3.2340.4494860.3395742X-RAY DIFFRACTION46
3.234-3.38110.33351210.3091130X-RAY DIFFRACTION70
3.3811-3.55920.33221560.26461420X-RAY DIFFRACTION88
3.5592-3.7820.31071730.23761527X-RAY DIFFRACTION94
3.782-4.07370.24481720.21211588X-RAY DIFFRACTION99
4.0737-4.4830.23891810.18881623X-RAY DIFFRACTION100
4.483-5.13020.27221800.19361623X-RAY DIFFRACTION100
5.1302-6.45770.26791810.23291641X-RAY DIFFRACTION100
6.4577-36.61560.2751770.22321634X-RAY DIFFRACTION97

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