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- PDB-8bq7: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 8bq7
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH2829
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / OGG1
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / 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 oxidative stress / microtubule binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / DNA damage response / regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus
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
NICKEL (II) ION / Chem-R4U / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsScaletti, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1
Authors: Hank, E.C. / D’Arcy-Evans, N.D. / Scaletti, E.R. / Benitez-Buelga, C. / Wallner, O. / Ortis, F. / Zhou, K. / Meng, L. / del Prado, A. / Calvo, P. / Almlof, I. / Wiita, E. / Nierlin, K. ...Authors: Hank, E.C. / D’Arcy-Evans, N.D. / Scaletti, E.R. / Benitez-Buelga, C. / Wallner, O. / Ortis, F. / Zhou, K. / Meng, L. / del Prado, A. / Calvo, P. / Almlof, I. / Wiita, E. / Nierlin, K. / Kosenina, S. / Kramer, A. / Eddershaw, A. / Kehler, M. / Long, M. / Jemth, A.S. / Dawson, H. / Stewart, J. / Dickey, A. / Astorga, M.E. / Varga, M. / Homan, E.J. / Scobie, M. / Knapp, S. / Sastre, L. / Stenmark, P. / de Vega, M. / Helleday, T. / Michel, M.
History
DepositionNov 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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: N-glycosylase/DNA lyase
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8336
Polymers107,4503
Non-polymers3833
Water1,11762
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1083
Polymers35,8171
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9092
Polymers35,8171
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-glycosylase/DNA lyase


Theoretical massNumber of molelcules
Total (without water)35,8171
Polymers35,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.733, 82.095, 169.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-glycosylase/DNA lyase


Mass: 35816.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ogg1 / Production host: Escherichia coli (E. coli)
References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-R4U / ~{N}4-cyclohexyl-2~{H}-pyrazolo[3,4-d]pyrimidine-4,6-diamine


Mass: 232.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 10 % w/v PEG4000, 20 % glycerol, 0.02 M monosaccharide, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.6→72.993 Å / Num. obs: 35462 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 4247 / CC1/2: 0.589

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PZ1

7pz1


Resolution: 2.6→72.993 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.299 / WRfactor Rwork: 0.255 / SU B: 15.94 / SU ML: 0.328 / Average fsc free: 0.9274 / Average fsc work: 0.9445 / Cross valid method: FREE R-VALUE / ESU R: 0.769 / ESU R Free: 0.372
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3069 1773 5.011 %
Rwork0.2549 33611 -
all0.257 --
obs-35384 99.918 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 75.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.401 Å2-0 Å2-0 Å2
2--2.914 Å2-0 Å2
3----2.514 Å2
Refinement stepCycle: LAST / Resolution: 2.6→72.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6953 0 24 62 7039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0117183
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166223
X-RAY DIFFRACTIONr_angle_refined_deg0.6531.6479824
X-RAY DIFFRACTIONr_angle_other_deg0.2331.56314381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3755906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.543548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65310994
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.19510310
X-RAY DIFFRACTIONr_chiral_restr0.0320.21085
X-RAY DIFFRACTIONr_chiral_restr_other0.010.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021525
X-RAY DIFFRACTIONr_nbd_refined0.170.21450
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.25941
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23548
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2143
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.210
X-RAY DIFFRACTIONr_nbd_other0.1360.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0540.22
X-RAY DIFFRACTIONr_mcbond_it1.9838.5243648
X-RAY DIFFRACTIONr_mcbond_other1.9818.5253648
X-RAY DIFFRACTIONr_mcangle_it3.47412.7714546
X-RAY DIFFRACTIONr_mcangle_other3.47312.7734547
X-RAY DIFFRACTIONr_scbond_it1.5128.2843535
X-RAY DIFFRACTIONr_scbond_other1.5128.2853536
X-RAY DIFFRACTIONr_scangle_it2.66612.4475278
X-RAY DIFFRACTIONr_scangle_other2.66612.4485279
X-RAY DIFFRACTIONr_lrange_it5.672102.1568011
X-RAY DIFFRACTIONr_lrange_other5.665102.178009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.6-2.6680.4261350.37424310.37725740.8690.89999.68920.371
2.668-2.7410.3431320.35323770.35325130.9140.91799.84080.343
2.741-2.820.3511170.33923200.33924380.9160.92699.9590.323
2.82-2.9060.371250.33122330.33423590.9110.92899.95760.307
2.906-3.0020.3481180.29421940.29723130.9260.93999.95680.271
3.002-3.1070.3251110.28921390.29122500.9270.9441000.265
3.107-3.2240.3481250.29220150.29521400.9110.9441000.267
3.224-3.3550.32870.27620010.27820880.9370.9511000.253
3.355-3.5040.3081030.27818990.2820020.9420.951000.26
3.504-3.6750.287800.25918260.2619070.9510.95999.94760.241
3.675-3.8730.324830.25817530.26118360.9330.9581000.242
3.873-4.1070.295820.24516580.24717410.9480.96399.94260.237
4.107-4.390.265950.24115190.24216140.9540.9641000.238
4.39-4.740.285850.22114480.22415330.9510.9681000.22
4.74-5.190.264790.22813400.2314190.9590.9661000.232
5.19-5.7990.428580.23912290.24712870.8940.9641000.244
5.799-6.6890.376420.25411050.25911470.9290.9571000.258
6.689-8.1760.238620.2029350.2049970.9670.9731000.215
8.176-11.490.23370.1717390.1737760.9630.981000.189
11.49-72.9930.373170.3294500.3314770.9210.89997.90360.605

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