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Yorodumi- PDB-8cey: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cey | |||||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH11233 | |||||||||
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: 1.95 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 TH11233 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 | 8cey.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cey.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 8cey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/8cey ftp://data.pdbj.org/pub/pdb/validation_reports/ce/8cey | 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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1 |
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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 | Mass: 249.332 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15N3OS / 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: 2.77 Å3/Da / Density % sol: 55.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% w/v PEG4000, 20% v/v glycerol, 0.03M of each halide, 0.1M MES/imidazole pH 6.5. Morpheus screen, Molecular dimensions. |
-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 XE 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: 1.95→59.077 Å / Num. obs: 83828 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 14 % / Num. unique obs: 4543 / CC1/2: 0.372 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G3Y Resolution: 1.95→59.077 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.235 / Average fsc free: 0.9189 / Average fsc work: 0.9346 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.173 / 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: 54.783 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→59.077 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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