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Yorodumi- PDB-4ofa: Structural basis for thymine glycosylase activity on T:O6-methylG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ofa | ||||||
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Title | Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / mismatch / thymine glycosylase / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol ...satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol / nuclear speck / DNA repair / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Ouzon-Shubeita, H. / Lin, Y.-L. / Lee, S. | ||||||
Citation | Journal: To be Published Title: Structure of MBD4 bound to G:T mispair DNA Authors: Ouzon-Shubeita, H. / Lin, Y.-L. / Lee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ofa.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ofa.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ofa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/4ofa ftp://data.pdbj.org/pub/pdb/validation_reports/of/4ofa | HTTPS FTP |
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-Related structure data
Related structure data | 4e9gS 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: 22486.846 Da / Num. of mol.: 1 / Fragment: catalytic domain of MBD4 / Mutation: D560N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: DNA chain | Mass: 3648.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nature substrate |
#3: DNA chain | Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nature substrate |
#4: Chemical | ChemComp-MG / |
#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: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 33% ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2012 |
Radiation | Monochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 35660 / % possible obs: 99.6 % / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4E9G Resolution: 1.55→38.03 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.131 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.069 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.955 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→38.03 Å
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