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- PDB-4z47: Structure of the enzyme-product complex resulting from TDG action... -

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Basic information

Entry
Database: PDB / ID: 4z47
TitleStructure of the enzyme-product complex resulting from TDG action on a GU mismatch in the presence of excess base
Components
  • (DNA) x 2
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsDNA binding protein/DNA / protein-DNA complex / DNA binding protein-DNA complex
Function / homology
Function and homology information


thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / 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 ...thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / 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 / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 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
ACETIC ACID / DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsPozharski, E. / Malik, S.S. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM72711 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Authors: Malik, S.S. / Coey, C.T. / Varney, K.M. / Pozharski, E. / Drohat, A.C.
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G/T mismatch-specific thymine DNA glycosylase
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4377
Polymers40,1913
Non-polymers2464
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-14 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.305, 53.322, 82.297
Angle α, β, γ (deg.)90.000, 95.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-140-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein G/T mismatch-specific thymine DNA glycosylase / Thymine-DNA glycosylase / hTDG


Mass: 23070.670 Da / Num. of mol.: 1 / 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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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA


Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 8473.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 277 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.73 Å / Num. obs: 64847 / % possible obs: 94.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Net I/σ(I): 15.9 / Num. measured all: 760039 / Scaling rejects: 107
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obs
1.45-1.47111.23301329910.6450.72289.8
7.94-45.7313.851.463114570.9950.01899.60.067

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.4data scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNC

4fnc


Resolution: 1.45→45.73 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.2086 / WRfactor Rwork: 0.1464 / FOM work R set: 0.7863 / SU ML: 0.0604 / SU R Cruickshank DPI: 0.0629 / SU Rfree: 0.0652 / Cross valid method: THROUGHOUT / SU Rfree Cruickshank DPI: 0.0652 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 3110 4.8 %RANDOM
Rwork0.1403 ---
obs0.1428 61716 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.35 Å2 / Biso mean: 37.444 Å2 / Biso min: 17.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-0.65 Å2
2---0.28 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 1.45→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 1135 16 277 2985
Biso mean--37.06 47.1 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0162961
X-RAY DIFFRACTIONr_bond_other_d0.0020.022240
X-RAY DIFFRACTIONr_angle_refined_deg2.2741.5954248
X-RAY DIFFRACTIONr_angle_other_deg1.91935214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63824.05474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32915291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.134158
X-RAY DIFFRACTIONr_chiral_restr0.1510.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0212523
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02667
X-RAY DIFFRACTIONr_mcbond_it4.9613.041796
X-RAY DIFFRACTIONr_mcbond_other4.9383.037794
X-RAY DIFFRACTIONr_mcangle_it6.3994.574994
X-RAY DIFFRACTIONr_rigid_bond_restr5.98535199
X-RAY DIFFRACTIONr_sphericity_free29.915591
X-RAY DIFFRACTIONr_sphericity_bonded18.99855205
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 207 -
Rwork0.314 4497 -
all-4704 -
obs--93.15 %

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