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- PDB-4ea4: Structure of the glycosylase domain of MBD4 bound to 5hmU-contain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ea4 | ||||||
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Title | Structure of the glycosylase domain of MBD4 bound to 5hmU-containing DNA | ||||||
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![]() | HYDROLASE/DNA / HhH DNA glycosylase family / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Vigouroux, A. | ||||||
![]() | ![]() Title: Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA. Authors: Morera, S. / Grin, I. / Vigouroux, A. / Couve, S. / Henriot, V. / Saparbaev, M. / Ishchenko, A.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 448 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e9eSC ![]() 4e9fC ![]() 4e9gC ![]() 4e9hC ![]() 4ea5C S: Starting model for refinement C: citing same article ( |
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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: Protein | Mass: 18713.615 Da / Num. of mol.: 1 / Fragment: glycosylase domain of MBD4 (residues 426-580) / Mutation: D560A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: DNA chain | Mass: 3664.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA |
#3: DNA chain | Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4000, 0.1 M Nacitrate, 20% isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→38 Å / Num. all: 16600 / Num. obs: 16435 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.12 Å / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4E9E Resolution: 2→37.91 Å / Cor.coef. Fo:Fc: 0.9316 / Cor.coef. Fo:Fc free: 0.9033 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.14 Å / Total num. of bins used: 8
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