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- PDB-6g3y: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g3y | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH5675 | ||||||
![]() | N-glycosylase/DNA lyase | ||||||
![]() | DNA BINDING PROTEIN / N-glycosylase / DNA lyase | ||||||
Function / homology | ![]() 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 / 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 / DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / 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 / response to radiation / base-excision repair / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Masuyer, G. / Helleday, T. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.9 KB | Display | ![]() |
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PDB format | ![]() | 160.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g3xC ![]() 1ebmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase #2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.09 M Halogens, 0.1 M Buffer System 2 pH 7.5, 50 % v/v Precipitant Mix 3 (Morpheus screen, Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→84.58 Å / Num. obs: 38585 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.976 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.126 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.51→2.56 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1719 / CC1/2: 0.137 / Rpim(I) all: 0.338 / Rrim(I) all: 0.918 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EBM Resolution: 2.51→84.58 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.199 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.702 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.336 Å2
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Refinement step | Cycle: 1 / Resolution: 2.51→84.58 Å
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Refine LS restraints |
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