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Yorodumi- PDB-2xhi: Separation-of-function mutants unravel the dual reaction mode of ... -
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-Basic information
Entry | Database: PDB / ID: 2xhi | ||||||
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Title | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | ||||||
Components |
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Keywords | LYASE/DNA / LYASE-DNA COMPLEX / SEPARATION-OF-FUNCTION MUTANT / HELIX-HAIRPIN-HELIX / DNA REPAIR | ||||||
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: 1.55 Å | ||||||
Authors | Dalhus, B. / Forsbring, M. / Helle, I.H. / Backe, P.H. / Forstrom, R.J. / Alseth, I. / Bjoras, M. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Separation-of-Function Mutants Unravel the Dual- Reaction Mode of Human 8-Oxoguanine DNA Glycosylase. Authors: Dalhus, B. / Forsbring, M. / Helle, I.H. / Vik, E.S. / Forstrom, R.J. / Backe, P.H. / Alseth, I. / Bjoras, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xhi.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xhi.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xhi_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 2xhi_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 2xhi_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 2xhi_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/2xhi ftp://data.pdbj.org/pub/pdb/validation_reports/xh/2xhi | HTTPS FTP |
-Related structure data
Related structure data | 1yqrS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40565.961 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase | ||||
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#2: DNA chain | Mass: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: DNA chain | Mass: 4561.948 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 249 TO CYS ENGINEERED RESIDUE IN CHAIN A, CYS 253 TO LYS ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.4 Å / Num. obs: 77880 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.58 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YQR Resolution: 1.55→24.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.827 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.746 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→24.63 Å
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