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- PDB-7az0: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7az0
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with TH12161
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / 8-oxoguanine DNA glycosylase / N-glycosylase / DNA lyase / DNA repair
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-SDW / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDavies, J.R. / Masuyer, G. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Science / Year: 2022
Title: Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function.
Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / ...Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / Visnes, T. / Sastre-Perona, A. / Danda, A.N. / Homan, E.J. / Marimuthu, K. / Zhenjun, Z. / Chi, C.N. / Sarno, A. / Wiita, E. / von Nicolai, C. / Komor, A.J. / Rajagopal, V. / Muller, S. / Hank, E.C. / Varga, M. / Scaletti, E.R. / Pandey, M. / Karsten, S. / Haslene-Hox, H. / Loevenich, S. / Marttila, P. / Rasti, A. / Mamonov, K. / Ortis, F. / Schomberg, F. / Loseva, O. / Stewart, J. / D'Arcy-Evans, N. / Koolmeister, T. / Henriksson, M. / Michel, D. / de Ory, A. / Acero, L. / Calvete, O. / Scobie, M. / Hertweck, C. / Vilotijevic, I. / Kalderen, C. / Osorio, A. / Perona, R. / Stolz, A. / Stenmark, P. / Berglund, U.W. / de Vega, M. / Helleday, T.
History
DepositionNov 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: N-glycosylase/DNA lyase
BBB: N-glycosylase/DNA lyase
CCC: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2836
Polymers107,4503
Non-polymers8333
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-16 kcal/mol
Surface area41710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.086, 81.645, 169.631
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
11Chains AAA BBB
22Chains AAA CCC
33Chains BBB CCC

NCS ensembles :
ID
1
2
3

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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-SDW / 2-cyclopropyl-~{N}-(4-iodophenyl)quinazolin-4-amine


Mass: 387.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14IN3 / 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.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 52.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 30% v/v Precipitant Mix 2 (Morpheus Screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→81.64 Å / Num. obs: 44894 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4638 / CC1/2: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.4→73.676 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.766 / SU ML: 0.251 / Cross valid method: FREE R-VALUE / ESU R: 0.43 / ESU R Free: 0.262
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 2164 4.829 %Random selection
Rwork0.2296 42651 --
all0.231 ---
obs-44815 99.973 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.957 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2---0.705 Å20 Å2
3---2.675 Å2
Refinement stepCycle: LAST / Resolution: 2.4→73.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 43 43 7481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176927
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.63210415
X-RAY DIFFRACTIONr_angle_other_deg1.1361.57516018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64721.017423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.436151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8661562
X-RAY DIFFRACTIONr_chiral_restr0.0520.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021738
X-RAY DIFFRACTIONr_nbd_refined0.1830.21321
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.26118
X-RAY DIFFRACTIONr_nbtor_refined0.1560.23601
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2138
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.229
X-RAY DIFFRACTIONr_nbd_other0.2070.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.23
X-RAY DIFFRACTIONr_mcbond_it2.9837.0323708
X-RAY DIFFRACTIONr_mcbond_other2.9837.0313707
X-RAY DIFFRACTIONr_mcangle_it4.80410.5384621
X-RAY DIFFRACTIONr_mcangle_other4.80410.544622
X-RAY DIFFRACTIONr_scbond_it2.637.2293943
X-RAY DIFFRACTIONr_scbond_other2.637.233944
X-RAY DIFFRACTIONr_scangle_it4.36410.7385788
X-RAY DIFFRACTIONr_scangle_other4.36310.7395789
X-RAY DIFFRACTIONr_lrange_it6.96278.5358211
X-RAY DIFFRACTIONr_lrange_other6.96378.5348210
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.059923
X-RAY DIFFRACTIONr_ncsr_local_group_20.10.059554
X-RAY DIFFRACTIONr_ncsr_local_group_30.10.059648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.4191720.363080X-RAY DIFFRACTION99.9078
2.462-2.530.3561440.3373044X-RAY DIFFRACTION99.8434
2.53-2.6030.3541480.3192933X-RAY DIFFRACTION100
2.603-2.6830.3571700.3272842X-RAY DIFFRACTION99.9668
2.683-2.7710.3111350.3032801X-RAY DIFFRACTION100
2.771-2.8680.3161720.32638X-RAY DIFFRACTION100
2.868-2.9760.3291140.2892628X-RAY DIFFRACTION100
2.976-3.0980.3321210.2722513X-RAY DIFFRACTION100
3.098-3.2350.3421370.2832400X-RAY DIFFRACTION99.9212
3.235-3.3930.2591030.2582331X-RAY DIFFRACTION100
3.393-3.5760.2881030.2412205X-RAY DIFFRACTION100
3.576-3.7930.2151060.2212071X-RAY DIFFRACTION100
3.793-4.0540.2441240.2181958X-RAY DIFFRACTION100
4.054-4.3780.232750.1971854X-RAY DIFFRACTION100
4.378-4.7940.267780.1841727X-RAY DIFFRACTION100
4.794-5.3580.176690.1781546X-RAY DIFFRACTION100
5.358-6.1830.247640.2051381X-RAY DIFFRACTION100
6.183-7.5620.24480.1921203X-RAY DIFFRACTION100
7.562-10.6530.133490.158933X-RAY DIFFRACTION100
10.653-73.6760.21320.225563X-RAY DIFFRACTION99.8322

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