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- PDB-9f8z: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 9f8z
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13677
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 / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsScaletti, 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 TH13677
Authors: Scaletti, E. / Stenmark, P.
History
DepositionMay 7, 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

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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)108,1887
Polymers107,4503
Non-polymers7384
Water43224
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2634
Polymers35,8171
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1082
Polymers35,8171
Non-polymers2921
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)80.643, 82.369, 171.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111GLNGLN10 - 3253 - 318
211GLNGLN10 - 3253 - 318
322LEULEU10 - 3233 - 316
422LEULEU10 - 3233 - 316
533LEULEU10 - 3233 - 316
633LEULEU10 - 3233 - 316

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-A1IBJ / ~{N}4-(5-chloranyl-6-methoxy-pyridin-3-yl)-1~{H}-pyrazolo[3,4-d]pyrimidine-4,6-diamine


Mass: 291.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10ClN7O / 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.: 24 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene Glycols, 0.1 M sodium HEPES/MOPS pH 7.5, 50 % GOL_P4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→85.9 Å / Num. obs: 31051 / % possible obs: 94.1 % / Redundancy: 13.8 % / CC1/2: 1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.71 Å / Num. unique obs: 1553 / CC1/2: 0.705

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.503→85.9 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 14.767 / SU ML: 0.311 / Cross valid method: FREE R-VALUE / ESU R Free: 0.39
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2771 1505 4.847 %
Rwork0.2252 29545 -
all0.228 --
obs-31050 77.099 %
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: 68.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.462 Å2-0 Å20 Å2
2---0.534 Å20 Å2
3---0.071 Å2
Refinement stepCycle: LAST / Resolution: 2.503→85.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 46 24 7589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167170
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.65410594
X-RAY DIFFRACTIONr_angle_other_deg0.431.57716441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8775943
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.62563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.105101217
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.49810370
X-RAY DIFFRACTIONr_chiral_restr0.060.21127
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021929
X-RAY DIFFRACTIONr_nbd_refined0.2240.21725
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.26794
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23813
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.219
X-RAY DIFFRACTIONr_nbd_other0.2240.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.21
X-RAY DIFFRACTIONr_mcbond_it6.5426.8173784
X-RAY DIFFRACTIONr_mcbond_other6.5416.8173784
X-RAY DIFFRACTIONr_mcangle_it10.04412.2294723
X-RAY DIFFRACTIONr_mcangle_other10.04512.2294724
X-RAY DIFFRACTIONr_scbond_it6.2367.1323995
X-RAY DIFFRACTIONr_scbond_other6.2027.133992
X-RAY DIFFRACTIONr_scangle_it9.78612.8645871
X-RAY DIFFRACTIONr_scangle_other9.76112.865866
X-RAY DIFFRACTIONr_lrange_it13.47965.4348897
X-RAY DIFFRACTIONr_lrange_other13.47965.4448896
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.0510118
X-RAY DIFFRACTIONr_ncsr_local_group_20.120.059850
X-RAY DIFFRACTIONr_ncsr_local_group_30.1140.059934
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.117270.05009
12AX-RAY DIFFRACTIONLocal ncs0.117270.05009
23AX-RAY DIFFRACTIONLocal ncs0.11990.05009
24AX-RAY DIFFRACTIONLocal ncs0.11990.05009
35AX-RAY DIFFRACTIONLocal ncs0.113720.05009
36AX-RAY DIFFRACTIONLocal ncs0.113720.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.5680.60250.30559X-RAY DIFFRACTION2.1865
2.568-2.6380.342180.311471X-RAY DIFFRACTION17.2792
2.638-2.7140.302480.318973X-RAY DIFFRACTION36.7266
2.714-2.7980.304930.3191387X-RAY DIFFRACTION54.2323
2.798-2.890.381880.3061790X-RAY DIFFRACTION72.1198
2.89-2.9910.3621380.3012143X-RAY DIFFRACTION89.4159
2.991-3.1040.333910.3042359X-RAY DIFFRACTION99.5126
3.104-3.230.3761190.2892259X-RAY DIFFRACTION100
3.23-3.3740.26950.2592165X-RAY DIFFRACTION100
3.374-3.5380.3031060.2542073X-RAY DIFFRACTION100
3.538-3.7290.3051040.2351979X-RAY DIFFRACTION100
3.729-3.9550.283670.2261906X-RAY DIFFRACTION100
3.955-4.2270.2481000.2051760X-RAY DIFFRACTION100
4.227-4.5650.293680.1881671X-RAY DIFFRACTION100
4.565-4.9990.233870.1791516X-RAY DIFFRACTION100
4.999-5.5870.236720.1831393X-RAY DIFFRACTION100
5.587-6.4470.291620.2021241X-RAY DIFFRACTION100
6.447-7.8840.229460.1821070X-RAY DIFFRACTION100
7.884-11.1040.194620.162825X-RAY DIFFRACTION100
11.104-85.90.296360.264505X-RAY DIFFRACTION99.4485

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