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- PDB-6w13: Human 8-oxoguanine glycosylase interrogating fully intrahelical o... -

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Basic information

Entry
Database: PDB / ID: 6w13
TitleHuman 8-oxoguanine glycosylase interrogating fully intrahelical oxoG lesion DNA
Components
  • DNA (5'-D(P*AP*CP*CP*TP*GP*G)-3')
  • DNA (5'-D(P*CP*AP*(8OG)P*GP*TP*CP*T)-3')
  • N-glycosylase/DNA lyase
KeywordsLyase/DNA / hOGG1 / 8-oxoG / Encounter complex / Interrogation complex / DNA BINDING PROTEIN / Lyase-DNA complex
Function / homology
Function and homology information


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / negative regulation of double-strand break repair via single-strand annealing / depurination / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / negative regulation of double-strand break repair via single-strand annealing / depurination / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / cellular response to cadmium ion / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
ACETATE ION / 2-(2-ethoxyethoxy)ethanethiol / DNA / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsShigdel, U. / Verdine, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2020
Title: The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.
Authors: Shigdel, U.K. / Ovchinnikov, V. / Lee, S.J. / Shih, J.A. / Karplus, M. / Nam, K. / Verdine, G.L.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: DNA (5'-D(P*CP*AP*(8OG)P*GP*TP*CP*T)-3')
C: DNA (5'-D(P*AP*CP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,97510
Polymers39,6093
Non-polymers3667
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-46 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.707, 90.707, 210.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-glycosylase/DNA lyase


Mass: 35670.355 Da / Num. of mol.: 1 / Mutation: E122Q, Y207C, C253W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(P*CP*AP*(8OG)P*GP*TP*CP*T)-3')


Mass: 2129.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*TP*GP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 92 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-S5Y / 2-(2-ethoxyethoxy)ethanethiol


Mass: 150.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate, pH 6.1, 200 mM MgOAc, and 17 % polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.38→45.35 Å / Num. obs: 21460 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 17
Reflection shellResolution: 2.38→2.51 Å / Rmerge(I) obs: 1.25 / Num. unique obs: 3038

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBM

1ebm


Resolution: 2.38→45.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.889 / SU B: 9.345 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.245
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1098 5.1 %RANDOM
Rwork0.2137 ---
obs0.2166 20290 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 193.95 Å2 / Biso mean: 52.078 Å2 / Biso min: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.38→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 267 28 85 2864
Biso mean--74.2 47.16 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0182830
X-RAY DIFFRACTIONr_bond_other_d0.0010.022486
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.8713905
X-RAY DIFFRACTIONr_angle_other_deg2.5935707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84523.214112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5521517
X-RAY DIFFRACTIONr_chiral_restr0.070.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213042
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02678
LS refinement shellResolution: 2.38→2.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 97 -
Rwork0.335 1438 -
all-1535 -
obs--99.61 %

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