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- PDB-2nob: Structure of catalytically inactive H270A human 8-oxoguanine glyc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nob | ||||||
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Title | Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA | ||||||
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![]() | Hydrolase / Lyase/DNA / N-glycosylase/DNA lyase / DNA repair / 8-oxoguanine / Lyase-DNA 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 / positive regulation of gene expression via chromosomal CpG island demethylation / 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 / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / 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 / 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 / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Radom, C.T. / Banerjee, A. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations. Authors: Radom, C.T. / Banerjee, A. / Verdine, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 451.6 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2noeC ![]() 2nofC ![]() 2nohC ![]() 2noiC ![]() 2nolC ![]() 2nozC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 4939.203 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 4561.948 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 36462.270 Da / Num. of mol.: 1 Fragment: 8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase Mutation: N149C,K249Q,H270A 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 | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.77 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Ca(OAc)2, Na cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 32157 / Num. obs: 32061 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.07 / Χ2: 1.044 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.491 / Num. unique all: 3082 / Χ2: 1.046 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 51.535 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.785 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Xplor file |
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