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- PDB-9hlf: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 9hlf
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14445
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 / 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
: / NICKEL (II) ION / PHOSPHATE ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsScaletti Hutchinson, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: Chemistry / Year: 2025
Title: Organocatalytic switches of DNA glycosylase OGG1 catalyze a highly efficient AP-lyase function.
Authors: Kehler, M. / Zhou, K. / Kemas, A.M. / Del Prado, A. / Hutchinson, E.S. / Nairn, E.H. / Varga, M. / Plattner, Y. / Zhong, Y. / Purewal-Sidhu, O. / Haslam, J. / Wiita, E. / Gildie, H. / ...Authors: Kehler, M. / Zhou, K. / Kemas, A.M. / Del Prado, A. / Hutchinson, E.S. / Nairn, E.H. / Varga, M. / Plattner, Y. / Zhong, Y. / Purewal-Sidhu, O. / Haslam, J. / Wiita, E. / Gildie, H. / Singerova, K. / Szaruga, Z. / Almlof, I. / Hormann, F.M. / Liu, K.C. / Wallner, O. / Ortis, F. / Homan, E.J. / Gileadi, O. / Rudd, S.G. / Stenmark, P. / de Vega, M. / Helleday, T. / D'Arcy-Evans, N.D. / Lauschke, V.M. / Michel, M.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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)107,9397
Polymers107,4503
Non-polymers4894
Water1,11762
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2094
Polymers35,8171
Non-polymers3933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9132
Polymers35,8171
Non-polymers961
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)80.760, 80.850, 170.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-A1IVU / ~{N}-(3,4-dichlorophenyl)pyridin-4-amine


Mass: 239.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8Cl2N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: MORPHEUS screen condition B9 (0.09 M Halogens, 0.1 M Tris/Bicine pH 8.5, 30 % P500MME_P20K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.64→85.424 Å / Num. obs: 33478 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellResolution: 2.64→2.69 Å / Num. unique obs: 1661 / CC1/2: 0.333

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→42.75 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 20.431 / SU ML: 0.391 / Cross valid method: THROUGHOUT / ESU R: 1.393 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29361 1760 5.3 %RANDOM
Rwork0.24582 ---
obs0.24832 31626 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.091 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å2-0 Å20 Å2
2---1.55 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.64→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 26 62 7474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127625
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167005
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.81610388
X-RAY DIFFRACTIONr_angle_other_deg0.3771.75216076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.1745.49261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45101175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0490.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021879
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_it2.6498.3953745
X-RAY DIFFRACTIONr_mcbond_other2.6498.3953745
X-RAY DIFFRACTIONr_mcangle_it4.60615.0814669
X-RAY DIFFRACTIONr_mcangle_other4.60615.0824670
X-RAY DIFFRACTIONr_scbond_it2.0918.4863880
X-RAY DIFFRACTIONr_scbond_other2.0878.4893873
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.75715.5535708
X-RAY DIFFRACTIONr_long_range_B_refined7.36881.38534
X-RAY DIFFRACTIONr_long_range_B_other7.36981.318532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.645→2.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 130 -
Rwork0.36 2233 -
obs--97.56 %

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