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Yorodumi- PDB-3ktu: Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ktu | ||||||
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Title | Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA | ||||||
Components |
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Keywords | HYDROLASE / LYASE/DNA / 8-oxoGuanine / 2'-fluoro-8-oxoGuanine / protein-DNA complex / DNA glycosylase / Base Excsion Repair / DNA damage / DNA repair / LYASE-DNA complex | ||||||
Function / homology | Function and homology information Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / negative regulation of double-strand break repair via single-strand annealing / depurination / 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 / negative regulation of double-strand break repair via single-strand annealing / depurination / 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 / 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 / base-excision repair / response to radiation / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Verdine, G.L. / Lee, S.M. | ||||||
Citation | Journal: to be published Title: Structural investigation of hOGG1 bound to a fluorinated oxoG analog Authors: Verdine, G.L. / Lee, S.M. #1: Journal: to be published Title: A Catalytic Checkpoint in Base Excision by the Human 8-Oxoguanine DNA Glycosylase hOGG1 Authors: Verdine, G.L. / Crenshaw, C.M. / Oo, K.S. / Kutchukian, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ktu.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ktu.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ktu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ktu_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 3ktu_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 3ktu_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3ktu_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3ktu ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3ktu | 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: 35727.469 Da / Num. of mol.: 1 / Fragment: sequence database residues 12-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMH, MUTM, OGG1, OGH1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase | ||
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#2: DNA chain | Mass: 4016.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 3672.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA / Source: (synth.) synthetic construct (others) | ||
#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: 3.03 Å3/Da / Density % sol: 59.39 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 6 Details: Calcium Chloride, Sodium Cacodylate, pH 6.0, PEG 8000, 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: 24-ID-C / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 24522 / % possible obs: 99.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.397 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EBM Resolution: 2.3→25.21 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 42.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.21 Å
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Refine LS restraints |
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Xplor file |
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