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Open data
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Basic information
Entry | Database: PDB / ID: 4e9e | ||||||
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Title | Structure of the glycosylase domain of MBD4 | ||||||
![]() | Methyl-CpG-binding domain protein 4 | ||||||
![]() | HYDROLASE / HhH DNA glycosylase superfamily | ||||||
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 | ![]() | 44.4 KB | Display | ![]() |
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PDB format | ![]() | 30.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411 KB | Display | ![]() |
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Full document | ![]() | 411 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e9fC ![]() 4e9gC ![]() 4e9hC ![]() 4ea4C ![]() 4ea5C ![]() 3ihoS 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: 19416.393 Da / Num. of mol.: 1 / Fragment: glycosylase domain of MBD4 (residues 426-580) 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 100 mM Tris-HCl and 0.2 M MgCl2, pH 8.5, 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: Jun 9, 2011 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.49 Å / Num. all: 14328 / Num. obs: 13475 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.25 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→2.02 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1661 / % possible all: 72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3IHO Resolution: 1.9→40.49 Å / Cor.coef. Fo:Fc: 0.9256 / Cor.coef. Fo:Fc free: 0.8986 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.252 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.05 Å / Total num. of bins used: 7
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