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- PDB-6u15: Human thymine DNA glycosylase N140A mutant bound to DNA with 2'-F... -

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Basic information

Entry
Database: PDB / ID: 6u15
TitleHuman thymine DNA glycosylase N140A mutant bound to DNA with 2'-F-5-carboxyl-dC substrate analog
Components
  • (DNA (28-MER)) x 2
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE / protein-DNA complex / HYDROLASE-DNA complex / DNA BINDING PROTEIN
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 ...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
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPidugu, L.S. / Pozharski, E. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase.
Authors: Pidugu, L.S. / Dai, Q. / Malik, S.S. / Pozharski, E. / Drohat, A.C.
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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 (28-MER)
D: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)43,1073
Polymers43,1073
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-30 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.220, 53.530, 82.500
Angle α, β, γ (deg.)90.000, 95.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 25831.984 Da / Num. of mol.: 1 / Mutation: N140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13569, thymine-DNA glycosylase
#2: DNA chain DNA (28-MER)


Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (28-MER)


Mass: 8628.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 3350, Ammonium Acetate, Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→46.37 Å / Num. obs: 15215 / % possible obs: 95 % / Redundancy: 5.8 % / Biso Wilson estimate: 64.01 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.162 / Rrim(I) all: 0.399 / Net I/σ(I): 4 / Num. measured all: 88089 / Scaling rejects: 379
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.495.89.194950816470.2144.16410.1330.597.3
8.98-46.376.20.09220123230.990.0390.112.698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U16

6u16


Resolution: 2.4→42.13 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.414 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.213 753 4.96 %RANDOM
Rwork0.199 ---
obs0.2 15179 94.5 %-
Displacement parametersBiso max: 140.59 Å2 / Biso mean: 65.55 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.5479 Å20 Å2-0.3649 Å2
2---11.1865 Å20 Å2
3---11.7344 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.4→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 1146 0 92 2724
Biso mean---60.16 -
Num. residues----251
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d797SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes314HARMONIC5
X-RAY DIFFRACTIONt_it2817HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2715SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2820HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4063HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion22.98
LS refinement shellResolution: 2.4→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 37
RfactorNum. reflection% reflection
Rfree0.1604 13 3.16 %
Rwork0.2294 398 -
all0.2268 411 -
obs--97.17 %
Refinement TLS params.Method: refined / Origin x: 19.116 Å / Origin y: -0.8195 Å / Origin z: 29.8212 Å
111213212223313233
T0.2958 Å20.0308 Å20.0716 Å2--0.304 Å20.0147 Å2---0.2958 Å2
L1.5184 °20.0145 °21.5701 °2-2.7279 °2-0.2411 °2--4.7706 °2
S-0.0635 Å °0.1686 Å °0.0345 Å °0.0966 Å °-0.1451 Å °0.0824 Å °0.1026 Å °0.4921 Å °0.2086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A109 - 303
2X-RAY DIFFRACTION1{ *|* }C109 - 303
3X-RAY DIFFRACTION1{ *|* }D109 - 303
4X-RAY DIFFRACTION1{ *|* }E109 - 303

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