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Yorodumi- PDB-4ew4: mouse MBD4 glycosylase domain in complex with DNA containing a ri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ew4 | |||||||||
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Title | mouse MBD4 glycosylase domain in complex with DNA containing a ribose sugar | |||||||||
Components |
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Keywords | HYDROLASE/DNA / stable intermediate / N-glycosidic bond / Helix-hairpin-Helix / DNA glycosylase / HYDROLASE-DNA complex | |||||||||
Function / homology | Function and homology information Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin ...Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin / DNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.791 Å | |||||||||
Authors | Hashimoto, H. / Zhang, X. / Cheng, X. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Authors: Hashimoto, H. / Zhang, X. / Cheng, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ew4.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ew4.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ew4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ew4_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 4ew4_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 4ew4_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4ew4_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/4ew4 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/4ew4 | HTTPS FTP |
-Related structure data
Related structure data | 4evvC 4ew0C 1ngnS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17564.195 Da / Num. of mol.: 1 / Fragment: glycosylase domain, UNP residues 411-554 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mbd4 / Plasmid: pXC1064 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Z2D7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide synthesis / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3225.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide synthesis / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 20 molecules
#4: Chemical | ChemComp-NI / |
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#5: Chemical | ChemComp-UNX / |
#6: 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: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 25% polyethylene glycol 3350, 200 mM NaCl, 100 mM BIS-TRIS-HCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2011 / Details: Si (220) |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.791→27.4 Å / Num. obs: 6818 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 78.66 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 2.791→2.94 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 3.7 / Num. unique all: 657 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NGN Resolution: 2.791→27.4 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.141 Å2 / ksol: 0.295 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.791→27.4 Å
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Refine LS restraints |
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LS refinement shell |
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