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- PDB-7zc7: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7zc7
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH012941
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / OGG1 / inhibitor
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / negative regulation of double-strand break repair via single-strand annealing / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / negative regulation of double-strand break repair via single-strand annealing / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / DNA N-glycosylase activity / oxidized purine nucleobase lesion DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to light stimulus / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to cadmium ion / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / response to estradiol / microtubule binding / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / response to xenobiotic stimulus / DNA repair / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / 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-IKL / NICKEL (II) ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDavies, J.R. / Scaletti, 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 TH012941
Authors: Davies, J.R. / Scaletti, E. / Stenmark, P.
History
DepositionMar 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 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

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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)108,2096
Polymers107,4503
Non-polymers7603
Water1,58588
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1672
Polymers35,8171
Non-polymers3501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8752
Polymers35,8171
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1672
Polymers35,8171
Non-polymers3501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.860, 81.739, 168.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-IKL / 2-[4-(3,5-dimethylpyrazol-1-yl)phenyl]-~{N}-(4,5,6,7-tetrahydro-1,2-benzoxazol-3-yl)ethanamide


Mass: 350.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.09M Halogens, 0.1M Buffer System 1 (pH 6.5), 30.0% (v/v) P500MME_P20K (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: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→168.2 Å / Num. obs: 50390 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 4567 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.3→84.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 12.042 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30633 2564 5.1 %RANDOM
Rwork0.23864 ---
obs0.242 47746 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.516 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---2.47 Å20 Å2
3---1.44 Å2
Refinement stepCycle: 1 / Resolution: 2.3→84.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 53 88 7427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197571
X-RAY DIFFRACTIONr_bond_other_d0.0020.027008
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.94510332
X-RAY DIFFRACTIONr_angle_other_deg1.02316015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2055930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29422.791344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.966151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7691559
X-RAY DIFFRACTIONr_chiral_restr0.0880.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218677
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021886
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_it5.3376.7623732
X-RAY DIFFRACTIONr_mcbond_other5.3336.7613731
X-RAY DIFFRACTIONr_mcangle_it7.87110.1294658
X-RAY DIFFRACTIONr_mcangle_other7.8710.134659
X-RAY DIFFRACTIONr_scbond_it5.0856.9633839
X-RAY DIFFRACTIONr_scbond_other5.0846.9643840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.62310.3245675
X-RAY DIFFRACTIONr_long_range_B_refined10.45353.3638383
X-RAY DIFFRACTIONr_long_range_B_other10.45753.378376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 186 -
Rwork0.362 3464 -
obs--100 %

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