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

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Basic information

Entry
Database: PDB / ID: 9gih
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14047
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / OGG1 / glycosylase
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 / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 Å
AuthorsScaletti Hutchinson, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: To Be Published
Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14047
Authors: Scaletti Hutchinson, E. / Stenmark, P.
History
DepositionAug 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 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)107,8846
Polymers107,4503
Non-polymers4343
Water1,856103
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2514
Polymers35,8171
Non-polymers4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
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)79.976, 80.764, 166.815
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 10 - 324 / Label seq-ID: 3 - 317

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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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-A1IL2 / ~{N}-(3,4-dichlorophenyl)-1~{H}-pyrazolo[3,4-b]pyridin-4-amine


Mass: 279.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8Cl2N4 / 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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.09M Halogens, 0.1M MOPS/HEPES-Na pH 7.5, 50% v/v EDO_P8K (Morpheus Screen, Molecular Dimensions).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.27→83.407 Å / Num. obs: 49693 / % possible obs: 98.1 % / Redundancy: 13.3 % / CC1/2: 0.989 / Net I/σ(I): 14.1
Reflection shellResolution: 2.27→2.31 Å / Num. unique obs: 2504 / CC1/2: 0.759

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.271→83.407 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.296 / SU ML: 0.215 / Cross valid method: FREE R-VALUE / ESU R: 0.325 / ESU R Free: 0.249
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2666 2417 4.868 %
Rwork0.2081 47236 -
all0.211 --
obs-49653 97.993 %
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: 62.272 Å2
Baniso -1Baniso -2Baniso -3
1--0.321 Å20 Å2-0 Å2
2--1.191 Å2-0 Å2
3----0.871 Å2
Refinement stepCycle: LAST / Resolution: 2.271→83.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 24 103 7603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127710
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167136
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.81910494
X-RAY DIFFRACTIONr_angle_other_deg0.5671.75716372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.0685.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.291101218
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.07210366
X-RAY DIFFRACTIONr_chiral_restr0.0770.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021912
X-RAY DIFFRACTIONr_nbd_refined0.2270.21573
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.26169
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23704
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3350.226
X-RAY DIFFRACTIONr_nbd_other0.230.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.29
X-RAY DIFFRACTIONr_mcbond_it6.315.9533755
X-RAY DIFFRACTIONr_mcbond_other6.3075.9543755
X-RAY DIFFRACTIONr_mcangle_it8.8910.6814685
X-RAY DIFFRACTIONr_mcangle_other8.89110.6834686
X-RAY DIFFRACTIONr_scbond_it7.2946.4833955
X-RAY DIFFRACTIONr_scbond_other7.1896.4833952
X-RAY DIFFRACTIONr_scangle_it10.3311.6115809
X-RAY DIFFRACTIONr_scangle_other10.28811.6055804
X-RAY DIFFRACTIONr_lrange_it12.8259.3798507
X-RAY DIFFRACTIONr_lrange_other12.80359.2738504
X-RAY DIFFRACTIONr_ncsr_local_group_10.1240.059791
X-RAY DIFFRACTIONr_ncsr_local_group_20.1360.059584
X-RAY DIFFRACTIONr_ncsr_local_group_30.1240.059499
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.123720.05008
12AX-RAY DIFFRACTIONLocal ncs0.123720.05008
23AX-RAY DIFFRACTIONLocal ncs0.13570.05007
24AX-RAY DIFFRACTIONLocal ncs0.13570.05007
35AX-RAY DIFFRACTIONLocal ncs0.124370.05008
36AX-RAY DIFFRACTIONLocal ncs0.124370.05008
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
2.271-2.330.3651580.33435030.33536830.8780.90599.40270.333
2.33-2.3940.3471630.29734180.335830.9170.93599.94420.297
2.394-2.4630.3271870.28533270.28735150.9240.94499.97150.28
2.463-2.5390.3261840.27332330.27634200.9320.94999.91230.261
2.539-2.6220.3311420.25231380.25532800.9220.9571000.235
2.622-2.7140.3281380.26527310.26832110.9310.94689.34910.235
2.714-2.8160.3521510.2329430.23630950.9280.96299.96770.201
2.816-2.9310.281490.21728350.2229840.9490.9691000.189
2.931-3.0610.291580.2227120.22328700.9410.9691000.194
3.061-3.210.3081120.21926360.22327480.9480.971000.198
3.21-3.3840.2521570.20524360.20825940.9630.97499.96140.188
3.384-3.5890.2691040.19621290.19924780.9580.97390.1130.18
3.589-3.8360.239980.18620560.18823560.9640.97591.42610.175
3.836-4.1430.221840.18618790.18721610.9710.97490.83760.175
4.143-4.5370.2241040.16619330.16920370.9650.9831000.17
4.537-5.070.239810.1817540.18318350.9650.9811000.19
5.07-5.8510.282710.20515620.20816330.9740.981000.216
5.851-7.1580.28810.20913240.21314050.9590.9741000.227
7.158-10.0850.172610.15210580.15311190.9820.9851000.183
10.085-83.4070.31340.2466290.2496630.9490.9571000.313

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