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Yorodumi- PDB-6cc8: Crystal structure MBD3 MBD domain in complex with methylated CpG DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cc8 | |||||||||
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Title | Crystal structure MBD3 MBD domain in complex with methylated CpG DNA | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information ventricular cardiac muscle tissue development / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Regulation of TP53 Activity through Acetylation ...ventricular cardiac muscle tissue development / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / 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 | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Liu, K. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: Febs J. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cc8.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cc8.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cc8_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 6cc8_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 6cc8_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 6cc8_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/6cc8 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/6cc8 | HTTPS FTP |
-Related structure data
Related structure data | 6ccgC 6ceuC 6cevC 6c2k 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8473.716 Da / Num. of mol.: 2 / Fragment: MBD domain (UNP residues 1-71) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBD3 / Plasmid: pET28-GSTLIC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O95983 #2: DNA chain | Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: dodecanucleotide / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35.73 Å / Num. obs: 25160 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.761 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6C2K 6c2k Resolution: 1.95→35.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.689 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.156 Details: MODEL WAS ORIGINALLY REFINED AGAINST DATA COLLECTED ON AN ISOMORPHOUS CRYSTAL. THAT STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING PHASER AND MOLREP TO POSITION FIRST AND SECOND COPY OF ...Details: MODEL WAS ORIGINALLY REFINED AGAINST DATA COLLECTED ON AN ISOMORPHOUS CRYSTAL. THAT STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING PHASER AND MOLREP TO POSITION FIRST AND SECOND COPY OF THE COMPLEX, RESPECTIVELY. REFMAC WAS USED DURING INTERMEDIATE REFINEMENT. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→35.73 Å
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