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Yorodumi- PDB-7z5b: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z5b | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013546 | ||||||
Components | N-glycosylase/DNA lyase | ||||||
Keywords | DNA BINDING PROTEIN / OGG1 / glycosylase / 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: 2.6 Å | ||||||
Authors | Scaletti, E. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: To Be Published Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013546 Authors: Scaletti, E. / Stenmark, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z5b.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z5b.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 7z5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/7z5b ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z5b | 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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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 | #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: 2.5 Å3/Da / Density % sol: 50.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.09 M Halogens, 0.1 M Buffer System 1 pH 6.5, 37.5 % v/v MPD_P1K_P3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→57.8 Å / Num. obs: 33992 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.994 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.6→2.72 Å / Num. unique obs: 4084 / CC1/2: 0.996 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G3Y Resolution: 2.6→82.96 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.903 / SU B: 21.355 / SU ML: 0.414 / Cross valid method: THROUGHOUT / ESU R: 1.251 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.664 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→82.96 Å
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