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- PDB-7z5r: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7z5r
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH012035
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / OGG1 / glycosylase / inhibitor
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 / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / cellular response to cadmium ion / response to light stimulus / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / cellular response to reactive oxygen species / response to radiation / base-excision repair / nuclear matrix / response to estradiol / microtubule binding / response to oxidative stress / response to ethanol / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA repair / 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
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
Chem-IGQ / NICKEL (II) ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, J.R. / Scaletti, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Virtual fragment screening for DNA repair inhibitors in vast chemical space.
Authors: Luttens, A. / Vo, D.D. / Scaletti, E.R. / Wiita, E. / Almlof, I. / Wallner, O. / Davies, J. / Kosenina, S. / Meng, L. / Long, M. / Mortusewicz, O. / Masuyer, G. / Ballante, F. / Michel, M. / ...Authors: Luttens, A. / Vo, D.D. / Scaletti, E.R. / Wiita, E. / Almlof, I. / Wallner, O. / Davies, J. / Kosenina, S. / Meng, L. / Long, M. / Mortusewicz, O. / Masuyer, G. / Ballante, F. / Michel, M. / Homan, E. / Scobie, M. / Kalderen, C. / Warpman Berglund, U. / Tarnovskiy, A.V. / Radchenko, D.S. / Moroz, Y.S. / Kihlberg, J. / Stenmark, P. / Helleday, T. / Carlsson, J.
History
DepositionMar 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 5, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _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)108,3147
Polymers107,4503
Non-polymers8644
Water2,288127
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1443
Polymers35,8171
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0852
Polymers35,8171
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0852
Polymers35,8171
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.459, 81.533, 170.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-IGQ / (7~{R})-~{N}-(4,5,6,7-tetrahydro-1,2-benzoxazol-3-yl)bicyclo[4.2.0]octa-1,3,5-triene-7-carboxamide


Mass: 268.310 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H16N2O2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Alcohols, 0.1M Buffer System 1 pH 6.5, 30.0 % v/v GOL_P4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→170.2 Å / Num. obs: 40059 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.997 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 4457 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.5→85.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.937 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29377 1960 4.9 %RANDOM
Rwork0.23667 ---
obs0.23946 37989 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2---1.63 Å20 Å2
3---0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.5→85.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7067 0 61 127 7255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197334
X-RAY DIFFRACTIONr_bond_other_d0.0020.026701
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.94110024
X-RAY DIFFRACTIONr_angle_other_deg0.925315254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77222.555317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.818151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841553
X-RAY DIFFRACTIONr_chiral_restr0.0640.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021839
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6527.2013673
X-RAY DIFFRACTIONr_mcbond_other3.6537.2013672
X-RAY DIFFRACTIONr_mcangle_it5.87810.7774572
X-RAY DIFFRACTIONr_mcangle_other5.87810.7784573
X-RAY DIFFRACTIONr_scbond_it3.1717.1683661
X-RAY DIFFRACTIONr_scbond_other3.177.1683662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.24810.7055447
X-RAY DIFFRACTIONr_long_range_B_refined8.40756.3878070
X-RAY DIFFRACTIONr_long_range_B_other8.40656.4038062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 166 -
Rwork0.376 2745 -
obs--99.66 %

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