+Open data
-Basic information
Entry | Database: PDB / ID: 1ko9 | ||||||
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Title | Native Structure of the Human 8-oxoguanine DNA Glycosylase hOGG1 | ||||||
Components | 8-oxoguanine DNA glycosylase | ||||||
Keywords | HYDROLASE / helix-hairpin-helix DNA-glycosylase | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Bjoras, M. / Seeberg, E. / Luna, L. / Pearl, L.H. / Barrett, T.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. Authors: Bjoras, M. / Seeberg, E. / Luna, L. / Pearl, L.H. / Barrett, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ko9.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ko9.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 1ko9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ko9_validation.pdf.gz | 382.6 KB | Display | wwPDB validaton report |
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Full document | 1ko9_full_validation.pdf.gz | 386.9 KB | Display | |
Data in XML | 1ko9_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1ko9_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1ko9 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1ko9 | HTTPS FTP |
-Related structure data
Related structure data | 1ebmS S: Starting model for refinement |
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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: Protein | Mass: 38834.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BK3010 References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||
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#2: Chemical | #3: 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: 1.97 Å3/Da / Density % sol: 37.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 4.6 Details: PEG 4000, Ammonium Sulphate, Sodium citrate, pH 4.6, Microbatch, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999 / Details: Sagitally focussing Ge (220) and a multilayer |
Radiation | Monochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→25 Å / Num. all: 17927 / Num. obs: 17891 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2402 / Rsym value: 0.215 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EBM Resolution: 2.15→23.07 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1610720.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Used maximum likelihood target in a simulated annealing/energy minimization procedure
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.698 Å2 / ksol: 0.358944 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→23.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.215 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.271 / Rfactor Rwork: 0.216 / Rfactor obs: 0.216 |