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- PDB-6g3x: Native Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 -

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Basic information

Entry
Database: PDB / ID: 6g3x
TitleNative Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / N-glycosylase / DNA lyase
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
TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain ...TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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: 2.1 Å
AuthorsMasuyer, G. / Helleday, T. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Science / Year: 2018
Title: Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.
Authors: Visnes, T. / Cazares-Korner, A. / Hao, W. / Wallner, O. / Masuyer, G. / Loseva, O. / Mortusewicz, O. / Wiita, E. / Sarno, A. / Manoilov, A. / Astorga-Wells, J. / Jemth, A.S. / Pan, L. / ...Authors: Visnes, T. / Cazares-Korner, A. / Hao, W. / Wallner, O. / Masuyer, G. / Loseva, O. / Mortusewicz, O. / Wiita, E. / Sarno, A. / Manoilov, A. / Astorga-Wells, J. / Jemth, A.S. / Pan, L. / Sanjiv, K. / Karsten, S. / Gokturk, C. / Grube, M. / Homan, E.J. / Hanna, B.M.F. / Paulin, C.B.J. / Pham, T. / Rasti, A. / Berglund, U.W. / von Nicolai, C. / Benitez-Buelga, C. / Koolmeister, T. / Ivanic, D. / Iliev, P. / Scobie, M. / Krokan, H.E. / Baranczewski, P. / Artursson, P. / Altun, M. / Jensen, A.J. / Kalderen, C. / Ba, X. / Zubarev, R.A. / Stenmark, P. / Boldogh, I. / Helleday, T.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)107,5094
Polymers107,4503
Non-polymers591
Water6,666370
1
A: 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
2
B: 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
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)80.769, 81.213, 167.531
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
Details: Recombinant construct of mouse OGG1 residues 11-325. Expressed with a cleavable N-terminal his tag (residues 8-10 from expression tag after cleavage)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ogg1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M Ethylene glycols, 0.1 M Buffer System 3 pH 8.5 and 50 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→83.77 Å / Num. obs: 68950 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Net I/σ(I): 16.9
Reflection shellResolution: 2.06→2.09 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 2 / Num. unique obs: 3260 / CC1/2: 0.334 / Rpim(I) all: 0.299 / Rrim(I) all: 0.93 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBM

1ebm


Resolution: 2.1→83.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.273 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27378 3139 4.9 %RANDOM
Rwork0.22116 ---
obs0.2237 61280 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.74 Å2
Refinement stepCycle: 1 / Resolution: 2.1→83.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7455 0 1 371 7827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197645
X-RAY DIFFRACTIONr_bond_other_d0.0010.026911
X-RAY DIFFRACTIONr_angle_refined_deg1.061.93710407
X-RAY DIFFRACTIONr_angle_other_deg0.739315977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66922.975363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.015151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9871562
X-RAY DIFFRACTIONr_chiral_restr0.0580.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021666
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_it1.9854.3633744
X-RAY DIFFRACTIONr_mcbond_other1.9834.3623743
X-RAY DIFFRACTIONr_mcangle_it3.3216.5274666
X-RAY DIFFRACTIONr_mcangle_other3.326.5284667
X-RAY DIFFRACTIONr_scbond_it1.9314.5423901
X-RAY DIFFRACTIONr_scbond_other1.9314.5433902
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2676.7245742
X-RAY DIFFRACTIONr_long_range_B_refined5.42850.7148760
X-RAY DIFFRACTIONr_long_range_B_other5.39650.648711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 210 -
Rwork0.387 4415 -
obs--96.76 %

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