+Open data
-Basic information
Entry | Database: PDB / ID: 7mwm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MBD2 with DNA | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN/DNA / DNA binding protein-DNA complex / MBD / TAM / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / siRNA binding / maternal behavior / methyl-CpG binding / C2H2 zinc finger domain binding / DNA methylation-dependent constitutive heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / siRNA binding / maternal behavior / methyl-CpG binding / C2H2 zinc finger domain binding / DNA methylation-dependent constitutive heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway / embryonic organ development / heterochromatin / response to mechanical stimulus / RNA Polymerase I Promoter Opening / response to nutrient levels / NoRC negatively regulates rRNA expression / Wnt signaling pathway / response to estradiol / regulation of cell population proliferation / protein-containing complex assembly / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Liu, K. / Dong, A. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of MBD2 with DNA Authors: Liu, K. / Dong, A. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mwm.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mwm.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 7mwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mwm_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7mwm_full_validation.pdf.gz | 456.6 KB | Display | |
Data in XML | 7mwm_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7mwm_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/7mwm ftp://data.pdbj.org/pub/pdb/validation_reports/mw/7mwm | HTTPS FTP |
-Related structure data
Related structure data | 7mwkC 7rayC 6c2e S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8763.156 Da / Num. of mol.: 2 / Fragment: UNP residues 143-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UBB5 #2: DNA chain | Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % / Mosaicity: 0.16 ° |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96863 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2013 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→41.81 Å / Num. obs: 86004 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Net I/σ(I): 14.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6C2E 6c2e Resolution: 1.601→31.068 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.69 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.61 Å2 / Biso mean: 25.5719 Å2 / Biso min: 11.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.601→31.068 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|