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Yorodumi- PDB-7pz1: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pz1 | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH8535 | ||||||
Components | N-glycosylase/DNA lyase | ||||||
Keywords | DNA 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 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Scaletti, E.R. / Helleday, T. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Chemmedchem / Year: 2023 Title: Optimization of N-Piperidinyl-Benzimidazolone Derivatives as Potent and Selective Inhibitors of 8-Oxo-Guanine DNA Glycosylase 1. Authors: Wallner, O. / Cazares-Korner, A. / Scaletti, E.R. / Masuyer, G. / Bekkhus, T. / Visnes, T. / Mamonov, K. / Ortis, F. / Lundback, T. / Volkova, M. / Koolmeister, T. / Wiita, E. / Loseva, O. / ...Authors: Wallner, O. / Cazares-Korner, A. / Scaletti, E.R. / Masuyer, G. / Bekkhus, T. / Visnes, T. / Mamonov, K. / Ortis, F. / Lundback, T. / Volkova, M. / Koolmeister, T. / Wiita, E. / Loseva, O. / Pandey, M. / Homan, E. / Benitez-Buelga, C. / Davies, J. / Scobie, M. / Warpman Berglund, U. / Kalderen, C. / Stenmark, P. / Helleday, T. / Michel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pz1.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pz1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/7pz1 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/7pz1 | HTTPS FTP |
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-Related structure data
Related structure data | 6g40SC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 3 molecules AAABBBCCC
#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 |
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-Non-polymers , 5 types, 79 molecules
#2: Chemical | ChemComp-8HA / |
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#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
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: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.12M Ethylene Glycols, 0.1M Buffer System 2 pH7.5, 30.0%v/v GOL_P4K (Morpheus screen, Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→84.8 Å / Num. obs: 42365 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.45→2.54 Å / Num. unique obs: 4385 / CC1/2: 0.53 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6g40 Resolution: 2.45→84.777 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.867 / SU ML: 0.333 / Cross valid method: FREE R-VALUE / ESU R: 0.504 / ESU R Free: 0.308 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.183 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→84.777 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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