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- PDB-1fn7: COUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fn7 | ||||||
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Title | COUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCISION DNA REPAIR PROTEIN | ||||||
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![]() | HYDROLASE/DNA / DNA REPAIR / DNA GLYCOSYLASE / PROTEIN/DNA / Helix hairpin helix / base recognition / oxoguanine / hydroxyguanine / base flipping / flipped-out base / extrahelical DNA / mechanism-based inhibitor / base-exicision repair / AP lyase / DNA glycosidase / HYDROLASE-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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Norman, D.P.G. / Bruner, S.D. / Verdine, G.L. | ||||||
![]() | ![]() Title: Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein. Authors: Norman, D.P. / Bruner, S.D. / Verdine, G.L. #1: ![]() Title: Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA Authors: Bruner, S.D. / Norman, D.P.G. / 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 | ![]() | 94.9 KB | Display | ![]() |
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PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.8 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4396.838 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 35648.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 16-18% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-1 / Detector: CCD / Date: Mar 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 18214 / Num. obs: 17653 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.74 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.54→2.69 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.352 / Num. unique all: 1757 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 83683 |
Reflection shell | *PLUS % possible obs: 99.8 % |
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Processing
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Refinement | Resolution: 2.6→29.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 294195.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 Details: conformation of the abasic deoxyribose ring was determined by modeling it as RNA (C3'-endo) and DNA (C2'-endo), and performing simulated annealing on both models. When modeled in the C2'- ...Details: conformation of the abasic deoxyribose ring was determined by modeling it as RNA (C3'-endo) and DNA (C2'-endo), and performing simulated annealing on both models. When modeled in the C2'-endo conformation, R and Rfree were lower, and the model fit the experimental Fo-Fc omit density better
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.06 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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