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Yorodumi- PDB-6g40: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g40 | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH9525 | ||||||
Components | N-glycosylase/DNA lyase | ||||||
Keywords | DNA 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 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Masuyer, G. / 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 | 6g40.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g40.ent.gz | 161.2 KB | Display | PDB format |
PDBx/mmJSON format | 6g40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g40 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g40 | HTTPS FTP |
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-Related structure data
Related structure data | 7pz1C 1ebmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
-Protein , 1 types, 3 molecules ABC
#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.) 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 |
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-Non-polymers , 5 types, 115 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-NI / | #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.12 M Monosaccharides, 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→81.34 Å / Num. obs: 39789 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.49→2.55 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2906 / CC1/2: 0.525 / Rpim(I) all: 0.396 / Rrim(I) all: 1.028 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EBM Resolution: 2.49→81.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.587 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.301 / 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: 82.556 Å2
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Refinement step | Cycle: 1 / Resolution: 2.49→81.34 Å
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Refine LS restraints |
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