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

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Basic information

Entry
Database: PDB / ID: 7qel
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH011247
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / glycosylase
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-AUS / NICKEL (II) ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, J.R. / Scaletti, E.R. / Stenmark, P.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Cancerfonden Sweden
CitationJournal: To Be Published
Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH011247
Authors: Davies, J.R. / Scaletti, E.R. / Stenmark, P.
History
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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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)108,2487
Polymers107,4503
Non-polymers7984
Water2,180121
1
AAA: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 36.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)36,1223
Polymers35,8171
Non-polymers3052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 36.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)36,0632
Polymers35,8171
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 36.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)36,0632
Polymers35,8171
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.350, 81.397, 168.405
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-AUS / (2~{R})-~{N}-(4,5,6,7-tetrahydro-1,2-benzoxazol-3-yl)spiro[2.3]hexane-2-carboxamide


Mass: 246.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H18N2O2 / 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.: 121 / 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: 52.59 %
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 GOL_P4K (Morpheus Screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.5→40.732 Å / Num. obs: 39517 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.996 / Net I/σ(I): 10.5
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4392 / CC1/2: 0.637

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G40

6g40


Resolution: 2.5→40.732 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.954 / SU ML: 0.282 / Cross valid method: FREE R-VALUE / ESU R: 0.605 / ESU R Free: 0.331
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2946 1906 4.831 %
Rwork0.2518 37546 -
all0.254 --
obs-39452 99.954 %
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: 56.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.654 Å20 Å20 Å2
2--1.223 Å20 Å2
3----0.569 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 55 121 7324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137425
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156752
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.64510154
X-RAY DIFFRACTIONr_angle_other_deg1.0581.58415432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.46321.037376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8361552
X-RAY DIFFRACTIONr_chiral_restr0.0360.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021815
X-RAY DIFFRACTIONr_nbd_refined0.1590.21409
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.26116
X-RAY DIFFRACTIONr_nbtor_refined0.1520.23489
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0630.217
X-RAY DIFFRACTIONr_nbd_other0.1520.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0720.24
X-RAY DIFFRACTIONr_mcbond_it1.26.33713
X-RAY DIFFRACTIONr_mcbond_other1.26.2993712
X-RAY DIFFRACTIONr_mcangle_it2.1899.4414629
X-RAY DIFFRACTIONr_mcangle_other2.1899.4424630
X-RAY DIFFRACTIONr_scbond_it0.7616.1853712
X-RAY DIFFRACTIONr_scbond_other0.766.1863713
X-RAY DIFFRACTIONr_scangle_it1.4529.2785510
X-RAY DIFFRACTIONr_scangle_other1.4529.2795511
X-RAY DIFFRACTIONr_lrange_it3.94771.7348075
X-RAY DIFFRACTIONr_lrange_other3.94171.7388070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.3711480.3292723X-RAY DIFFRACTION99.9652
2.565-2.6350.3431170.3132698X-RAY DIFFRACTION100
2.635-2.7110.3841270.3212597X-RAY DIFFRACTION100
2.711-2.7950.3491490.3072518X-RAY DIFFRACTION100
2.795-2.8860.3531480.2982399X-RAY DIFFRACTION100
2.886-2.9880.3661360.292333X-RAY DIFFRACTION99.9595
2.988-3.10.3171180.2872298X-RAY DIFFRACTION100
3.1-3.2270.3451200.2822201X-RAY DIFFRACTION100
3.227-3.370.3231110.282117X-RAY DIFFRACTION100
3.37-3.5340.287810.2552062X-RAY DIFFRACTION100
3.534-3.7250.245840.2321951X-RAY DIFFRACTION100
3.725-3.950.2641050.2311816X-RAY DIFFRACTION100
3.95-4.2220.263880.2251728X-RAY DIFFRACTION100
4.222-4.560.234750.221642X-RAY DIFFRACTION100
4.56-4.9930.237880.2171467X-RAY DIFFRACTION100
4.993-5.580.271770.241361X-RAY DIFFRACTION99.9305
5.58-6.4390.285520.2511235X-RAY DIFFRACTION100
6.439-7.8750.349330.2341060X-RAY DIFFRACTION100
7.875-11.0880.262240.196845X-RAY DIFFRACTION100
11.088-40.7320.349250.273495X-RAY DIFFRACTION97.1963

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