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- PDB-7z3y: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z3y | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545 | ||||||
![]() | N-glycosylase/DNA lyase | ||||||
![]() | DNA BINDING PROTEIN / glycosylase / inhibitor | ||||||
Function / homology | ![]() Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to light stimulus / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scaletti, E.R. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545 Authors: Scaletti, E.R. / Stenmark, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 714.7 KB | Display | ![]() |
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Full document | ![]() | 723.8 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 45.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g3yS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() ![]() References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase #2: Chemical | ChemComp-I9U / | #3: Chemical | #4: Chemical | ChemComp-NI / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.12M Alcohols, 0.1M Buffer System 2 pH 7.5, 30.0% v/v EDO_P8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.35→73 Å / Num. obs: 47609 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Num. unique obs: 4580 / CC1/2: 0.562 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6G3Y Resolution: 2.35→57.632 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.341 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / ESU R: 0.419 / ESU R Free: 0.298 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: 74.348 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→57.632 Å
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Refine LS restraints |
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LS refinement shell |
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