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- PDB-8xxg: Crystal structure of human 8-oxoguanine glycosylase K249H mutant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xxg | |||||||||||||||
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Title | Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 277 K for 2.5 hours | |||||||||||||||
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![]() | DNA/HYDROLASE / DNA repair / ROS / enzyme / intermediate / LYASE / DNA-HYDROLASE complex | |||||||||||||||
Function / homology | ![]() Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / 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 / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / 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 / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / 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 / endonuclease activity / microtubule binding / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Unno, M. / Koga, M. / Minowa, N. / Tanaka, Y. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Active residue mutation of hOGG1 provides a novel active mutant with an alternative reaction pathway Authors: Unno, M. / Morikawa, M. / Sychrovsky, V. / Koga, M. / Minowa, M. / Komuro, S. / Fukuta, M. / Tsuyuguchi, F. / Inamura, R. / Mano, H. / Nakashima, K. / Okamoto, Y. / Saio, T. / Hattori, Y. / Tanaka, Y. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798 KB | Display | ![]() |
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Full document | ![]() | 799.5 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xwcC ![]() 8xwuC ![]() 8xxkC C: citing same article ( |
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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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Unit cell |
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Components
-DNA chain , 3 types, 3 molecules CDG
#1: DNA chain | Mass: 2411.606 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 4939.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: DNA chain | Mass: 2073.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 37700.637 Da / Num. of mol.: 1 / Mutation: K249H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase |
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-Non-polymers , 4 types, 399 molecules 




#5: Chemical | ChemComp-A1LXK / [( Mass: 381.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O9P / Feature type: SUBJECT OF INVESTIGATION |
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#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-GOL / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: PEG 4000, MgCl2, Sodium cacodylate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→46.26 Å / Num. obs: 34366 / % possible obs: 98.4 % / Redundancy: 13.5 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.999 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.82→1.86 Å / Num. unique obs: 2018 / CC1/2: 0.992 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→46.26 Å
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Refine LS restraints |
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LS refinement shell |
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