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- PDB-5t2w: Structure of thymine DNA glycosylase bound to substrate analog 2'... -

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Basic information

Entry
Database: PDB / ID: 5t2w
TitleStructure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC
Components
  • DNA (27-MER)
  • DNA (28-MER)
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / protein-DNA complex / 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 ...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 / Resolution: 2.2 Å
AuthorsPidugu, L.S. / Pozharski, E. / Drohat, A.C.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase.
Authors: Pidugu, L.S. / Flowers, J.W. / Coey, C.T. / Pozharski, E. / Greenberg, M.M. / Drohat, A.C.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G/T mismatch-specific thymine DNA glycosylase
C: DNA (28-MER)
D: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)43,1183
Polymers43,1183
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.530, 51.900, 82.030
Angle α, β, γ (deg.)90.00, 101.52, 90.00
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: 25859.010 Da / Num. of mol.: 1 / Fragment: UNP residues 82-308
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
#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 (27-MER)


Mass: 8612.519 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.: 153 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→39.83 Å / Num. obs: 17671 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 39.1 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.17 / Net I/σ(I): 4.3
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.7 / CC1/2: 0.316 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HF7
Resolution: 2.2→21.37 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.8927 / SU R Cruickshank DPI: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.312 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.226 792 4.49 %RANDOM
Rwork0.1804 ---
obs0.1824 17639 99.96 %-
Displacement parametersBiso mean: 41.66 Å2
Baniso -1Baniso -2Baniso -3
1--8.5693 Å20 Å2-0.827 Å2
2---0.8026 Å20 Å2
3---9.372 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: 1 / Resolution: 2.2→21.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 1258 0 153 2952
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013015HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994343HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d870SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes303HARMONIC5
X-RAY DIFFRACTIONt_it3015HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion23.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3137SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2506 134 4.72 %
Rwork0.2302 2704 -
all0.2312 2838 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.4548-5.6009-2.96293.7734-0.17360.34110.00640.0291-0.1865-0.13260.1399-0.0476-0.15860.0095-0.14630.2048-0.0897-0.0287-0.04580.0293-0.088521.867-7.656139.3001
23.5013-2.02442.28341.0102-1.08764.09640.14920.0465-0.41630.0587-0.1098-0.15420.49080.5695-0.03940.10470.05050.0445-0.0355-0.01280.112917.8762-12.196428.4129
31.869-0.3911.14851.4985-0.35262.93680.0298-0.08120.02450.1456-0.03170.14890.3112-0.11240.0019-0.0687-0.02770.0431-0.0879-0.0176-0.05416.7318-4.027726.4881
44.9002-2.6314-1.14440.0081-0.48263.145-0.1617-0.5225-0.10790.04450.35870.3498-0.1893-0.3396-0.1970.0148-0.04920.037-0.01950.0284-0.05750.44542.399534.4749
54.2535-0.6261.03851.13110.39670.2466-0.10340.044-0.22270.27020.04280.23330.1689-0.34790.0606-0.0148-0.0480.0375-0.0676-0.0244-0.03990.4229-4.673225.8226
61.0068-1.9181-2.071.99122.9548-0.4051-0.05330.2178-0.1275-0.1919-0.1784-0.29150.38730.05520.2317-0.11630.00350.02490.0206-0.009-0.050719.5645-6.329322.9727
7-0.8703-0.96891.99392.8142-0.78881.52360.02960.11640.0737-0.6359-0.1888-0.32170.11920.53110.15930.02290.01980.10650.1842-0.030.010818.2548-2.993813.5762
80.6457-1.95890.11612.4458-0.57312.014-0.01480.3122-0.0898-0.2436-0.0949-0.01340.2051-0.04750.1097-0.1346-0.030.0388-0.0634-0.0281-0.16265.42510.833712.104
91.21990.4821-0.28181.14590.09541.7715-0.05850.31840.086-0.1460.01580.1675-0.1229-0.14180.04270.01680.00240.00890.0475-0.00120.01986.382510.278218.9385
10-2.1562-3.07255.04831.23293.30312.36850.07020.4998-0.0175-0.1957-0.11490.3239-0.4329-0.34990.0447-0.02460.0547-0.02930.09350.01130.0261-8.54039.654520.9165
114.19260.3531-3.35973.7322-0.47537.82490.32820.59440.4213-0.32010.2067-0.04030.0234-0.1644-0.5349-0.1869-0.11160.0564-0.1340.062-0.150423.409216.297611.6181
120.2764-0.17720.81323.814-2.19740.96980.0678-0.13280.01320.59910.09720.0463-0.5443-0.2007-0.16490.18090.0187-0.02670.00820.0147-0.107321.47141.174957.44
1313.45542.3914-0.099613.79096.42791.71220.176-0.7112-0.07610.8717-0.0653-0.3669-0.74290.9449-0.11070.1907-0.1593-0.0487-0.03790.0612-0.317326.4045-4.078870.298
141.09640.3346-0.90122.3558-1.50082.38160.02780.01780.07720.08030.0599-0.0247-0.17130.5812-0.0877-0.0742-0.03710.0177-0.08240.0002-0.081823.07139.50731.4277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|108 - A|112 }
2X-RAY DIFFRACTION2{ A|113 - A|126 }
3X-RAY DIFFRACTION3{ A|127 - A|158 }
4X-RAY DIFFRACTION4{ A|159 - A|176 }
5X-RAY DIFFRACTION5{ A|177 - A|193 }
6X-RAY DIFFRACTION6{ A|194 - A|198 }
7X-RAY DIFFRACTION7{ A|199 - A|214 }
8X-RAY DIFFRACTION8{ A|215 - A|244 }
9X-RAY DIFFRACTION9{ A|245 - A|290 }
10X-RAY DIFFRACTION10{ A|291 - A|302 }
11X-RAY DIFFRACTION11{ C|1 - C|12 }
12X-RAY DIFFRACTION12{ C|13 - C|28 }
13X-RAY DIFFRACTION13{ D|2 - D|7 }
14X-RAY DIFFRACTION14{ D|8 - D|28 }

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