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Open data
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Basic information
Entry | Database: PDB / ID: 6cnq | |||||||||
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Title | MBD2 in complex with methylated DNA | |||||||||
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![]() | TRANSCRIPTION/DNA / dna methylation / dna binding / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | ![]() satellite DNA binding / ventricular cardiac muscle tissue development / maternal behavior / NuRD complex / DNA methylation-dependent heterochromatin formation / siRNA binding / C2H2 zinc finger domain binding / methyl-CpG binding / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / maternal behavior / NuRD complex / DNA methylation-dependent heterochromatin formation / siRNA binding / C2H2 zinc finger domain binding / methyl-CpG binding / 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 | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, K. / Xu, C. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() Title: Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA. Authors: Liu, K. / Xu, C. / Lei, M. / Yang, A. / Loppnau, P. / Hughes, T.R. / Min, J. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.1 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
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Full document | ![]() | 454 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c1aC ![]() 6c1tC ![]() 6c1uC ![]() 6c1vC ![]() 6cnpC ![]() 6c2k 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8791.171 Da / Num. of mol.: 2 / Fragment: residues 143-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2M ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.15→40.58 Å / Num. obs: 20266 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.055 / Net I/σ(I): 18.1 / Num. measured all: 114295 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: earlier version of PDB entry 6C2K, unpublished DNA model ![]() 6c2k Resolution: 2.151→24.344 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.05 Details: arp/warp was used in map improvement mode. refmac was used at intermediate stages of refinement. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.47 Å2 / Biso mean: 63.028 Å2 / Biso min: 35.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.151→24.344 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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