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Yorodumi- PDB-2nol: Structure of catalytically inactive human 8-oxoguanine glycosylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nol | ||||||
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Title | Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxoG DNA | ||||||
Components |
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Keywords | Hydrolase / Lyase/DNA / N-glycosylase/DNA lyase / DNA repair / 8-oxoguanine / Lyase-DNA COMPLEX | ||||||
Function / homology | Function and homology information Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / 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 / depyrimidination / oxidized purine nucleobase lesion 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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / oxidized purine nucleobase lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / cellular response to cadmium ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / mitochondrial matrix / nuclear speck / response to xenobiotic stimulus / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Banerjee, A. / Radom, C.T. / Verdine, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nol.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nol.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 2nol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/2nol ftp://data.pdbj.org/pub/pdb/validation_reports/no/2nol | HTTPS FTP |
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-Related structure data
Related structure data | 2nobC 2noeC 2nofC 2nohC 2noiC 2nozC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4635.010 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: 36556.355 Da / Num. of mol.: 1 Fragment: 8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase Mutation: K249Q,S292C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.06 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, CaCl2, Na cacodylate, pH 6.0, 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2001 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.57→50 Å / Num. obs: 17596 / % possible obs: 99.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.132 / Χ2: 1.002 / Net I/σ(I): 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→50 Å / σ(F): 0
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Solvent computation | Bsol: 30.526 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→50 Å
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Refine LS restraints |
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Xplor file |
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