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Yorodumi- PDB-8cex: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
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-Basic information
Entry | Database: PDB / ID: 8cex | |||||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH11227 | |||||||||
Components | N-glycosylase/DNA lyase | |||||||||
Keywords | DNA BINDING PROTEIN / protein in complex with fragment 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 | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kosenina, S. / Scaletti, E.R. / Stenmark, P. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: To Be Published Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH11227 Authors: Kosenina, S. / Scaletti, E.R. / Stenmark, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cex.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cex.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 8cex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/8cex ftp://data.pdbj.org/pub/pdb/validation_reports/ce/8cex | HTTPS FTP |
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-Related structure data
Related structure data | 6g3yS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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 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-UG0 / | Mass: 244.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13FN2O / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% w/v PEG4000, 20% v/v glycerol, 0.03M of each ethylene glycol, 0.1M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→58.866 Å / Num. obs: 50891 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.057 / Rrim(I) all: 0.151 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.5 % / Num. unique obs: 4601 / CC1/2: 0.543 / Rrim(I) all: 2.221 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G3Y Resolution: 2.3→58.866 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.244 / Average fsc free: 0.9381 / Average fsc work: 0.9537 / Cross valid method: FREE R-VALUE / ESU R: 0.362 / ESU R Free: 0.256 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.536 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→58.866 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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