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- PDB-6cev: MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cev | ||||||
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Title | MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data | ||||||
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![]() | TRANSCRIPTION/DNA / Structural Genomics Consortium / SGC / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() ventricular cardiac muscle tissue development / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / methyl-CpG binding / DNA methylation-dependent heterochromatin formation / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 ...ventricular cardiac muscle tissue development / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / methyl-CpG binding / DNA methylation-dependent heterochromatin formation / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Regulation of TP53 Activity through Acetylation / response to nutrient levels / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / HDACs deacetylate histones / response to estradiol / in utero embryonic development / Potential therapeutics for SARS / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, K. / Tempel, W. / Wernimont, A.K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural analyses reveal that MBD3 is a methylated CG binder. Authors: Liu, K. / Lei, M. / Wu, Z. / Gan, B. / Cheng, H. / Li, Y. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.9 KB | Display | ![]() |
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PDB format | ![]() | 92.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6cc8SC ![]() 6ccgC ![]() 6ceuC C: citing same article ( S: Starting model for refinement |
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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: 8473.716 Da / Num. of mol.: 2 / Fragment: residues 1-71 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3662.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.2M sodium chloride, 0.1M bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2012 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→43.69 Å / Num. obs: 23289 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Net I/σ(I): 11.1 / Num. measured all: 84001 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: early version of model from PDB entry 6CC8 Resolution: 2.005→35.202 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.09 / Stereochemistry target values: ML Details: Electron density did not permit unambiguous distinction between strands of non-palindromic DNA. refmac was used for intermediate refinement steps. coot was used for interactive model ...Details: Electron density did not permit unambiguous distinction between strands of non-palindromic DNA. refmac was used for intermediate refinement steps. coot was used for interactive model building. Model geometry was validated with molprobity.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.05 Å2 / Biso mean: 43.3347 Å2 / Biso min: 23.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.005→35.202 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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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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