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- PDB-9gih: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
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Basic information
Entry | Database: PDB / ID: 9gih | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14047 | ||||||
![]() | N-glycosylase/DNA lyase | ||||||
![]() | DNA BINDING PROTEIN / OGG1 / glycosylase | ||||||
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 / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine 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 / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to oxidative stress / microtubule binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / DNA damage response / regulation of DNA-templated transcription / 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 Hutchinson, E. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14047 Authors: Scaletti Hutchinson, E. / 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 | ![]() | 371.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722.5 KB | Display | ![]() |
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Full document | ![]() | 735.9 KB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 10 - 324 / Label seq-ID: 3 - 317
NCS ensembles :
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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-A1IL2 / ~{ | Mass: 279.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8Cl2N4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.09M Halogens, 0.1M MOPS/HEPES-Na pH 7.5, 50% v/v EDO_P8K (Morpheus Screen, Molecular Dimensions). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 14, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→83.407 Å / Num. obs: 49693 / % possible obs: 98.1 % / Redundancy: 13.3 % / CC1/2: 0.989 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.27→2.31 Å / Num. unique obs: 2504 / CC1/2: 0.759 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 62.272 Å2
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Refinement step | Cycle: LAST / Resolution: 2.271→83.407 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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