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- PDB-7z3y: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7z3y
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / 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 / base-excision repair, AP site formation / 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 / base-excision repair, AP site formation / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / 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 / response to light stimulus / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-I9U / NICKEL (II) ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsScaletti, E.R. / 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 TH013545
Authors: Scaletti, E.R. / Stenmark, P.
History
DepositionMar 2, 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

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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)108,0797
Polymers107,4503
Non-polymers6294
Water2,288127
1
AAA: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 36.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)36,3544
Polymers35,8171
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 35.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)35,9092
Polymers35,8171
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: N-glycosylase/DNA lyase


  • defined by author
  • 35.8 kDa, 1 polymers
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)80.995, 81.831, 168.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-I9U / 2-[4-(3,5-dimethylpyrazol-1-yl)-2,6-bis(fluoranyl)phenyl]-~{N}-(4,5,6,7-tetrahydro-1,2-benzoxazol-3-yl)ethanamide


Mass: 386.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: 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

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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: 52.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.12M Alcohols, 0.1M Buffer System 2 pH 7.5, 30.0% v/v EDO_P8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→73 Å / Num. obs: 47609 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 4580 / CC1/2: 0.562

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.35→57.632 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.341 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / ESU R: 0.419 / ESU R Free: 0.298
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.31 2300 4.841 %
Rwork0.2597 45213 -
all0.262 --
obs-47513 99.91 %
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: 74.348 Å2
Baniso -1Baniso -2Baniso -3
1--2.078 Å20 Å20 Å2
2--1.807 Å20 Å2
3---0.271 Å2
Refinement stepCycle: LAST / Resolution: 2.35→57.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7121 0 41 127 7289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156686
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.63910069
X-RAY DIFFRACTIONr_angle_other_deg1.061.57715261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3545922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.54720.933375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.947151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.551553
X-RAY DIFFRACTIONr_chiral_restr0.0340.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021808
X-RAY DIFFRACTIONr_nbd_refined0.1530.21399
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1550.26141
X-RAY DIFFRACTIONr_nbtor_refined0.1490.23465
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0880.224
X-RAY DIFFRACTIONr_nbd_other0.1860.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.25
X-RAY DIFFRACTIONr_mcbond_it1.9238.2773709
X-RAY DIFFRACTIONr_mcbond_other1.9238.2763708
X-RAY DIFFRACTIONr_mcangle_it3.35212.4054624
X-RAY DIFFRACTIONr_mcangle_other3.35212.4074625
X-RAY DIFFRACTIONr_scbond_it1.4628.133663
X-RAY DIFFRACTIONr_scbond_other1.4628.1323664
X-RAY DIFFRACTIONr_scangle_it2.59312.1885445
X-RAY DIFFRACTIONr_scangle_other2.59312.1885445
X-RAY DIFFRACTIONr_lrange_it5.9894.4058026
X-RAY DIFFRACTIONr_lrange_other5.97194.4258020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.3531700.3813286X-RAY DIFFRACTION99.8555
2.411-2.4770.3681680.3533189X-RAY DIFFRACTION99.9107
2.477-2.5490.4231530.3583130X-RAY DIFFRACTION99.8783
2.549-2.6270.3581780.3463011X-RAY DIFFRACTION99.8747
2.627-2.7130.3741490.3182954X-RAY DIFFRACTION99.8713
2.713-2.8080.3931590.3152857X-RAY DIFFRACTION99.9669
2.808-2.9140.3751510.3062737X-RAY DIFFRACTION99.9308
2.914-3.0330.3481220.3042688X-RAY DIFFRACTION99.9644
3.033-3.1680.3611290.2982540X-RAY DIFFRACTION100
3.168-3.3220.4241120.2872452X-RAY DIFFRACTION99.961
3.322-3.5020.3321210.2822346X-RAY DIFFRACTION100
3.502-3.7140.2651110.2512232X-RAY DIFFRACTION100
3.714-3.9690.2661200.2452059X-RAY DIFFRACTION99.9541
3.969-4.2870.2711000.2411963X-RAY DIFFRACTION100
4.287-4.6950.321800.221812X-RAY DIFFRACTION100
4.695-5.2470.288720.2191645X-RAY DIFFRACTION100
5.247-6.0540.288690.2541481X-RAY DIFFRACTION100
6.054-7.4060.362500.2681257X-RAY DIFFRACTION100
7.406-10.4330.186490.182999X-RAY DIFFRACTION100
10.433-57.6320.328370.27575X-RAY DIFFRACTION97.4522

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