+Open data
-Basic information
Entry | Database: PDB / ID: 6vjw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of WT hMBD4 complexed with T:G mismatch DNA | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / MBD4 / T:G mismatch | ||||||
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: 2.02 Å | ||||||
Authors | Jung, H. / Lee, S. | ||||||
Citation | Journal: Biochem.J. / Year: 2020 Title: Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4. Authors: Ouzon-Shubeita, H. / Jung, H. / Lee, M.H. / Koag, M.C. / Lee, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vjw.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vjw.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vjw_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vjw_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 6vjw_validation.xml.gz | 9 KB | Display | |
Data in CIF | 6vjw_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/6vjw ftp://data.pdbj.org/pub/pdb/validation_reports/vj/6vjw | HTTPS FTP |
-Related structure data
Related structure data | 4e9gS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16612.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Production host: Escherichia coli (E. coli) References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
---|---|
#2: DNA chain | Mass: 3540.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: DNA chain | Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG1500 0.1 M MES pH 6.5 0.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→50 Å / Num. obs: 15766 / % possible obs: 97.7 % / Redundancy: 9.8 % / Rpim(I) all: 0.031 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 2.01→2.04 Å / Num. unique obs: 732 / CC1/2: 0.728 / Rpim(I) all: 0.524 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E9G Resolution: 2.02→38.24 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.45 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→38.24 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.15 Å
|