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Yorodumi- PDB-3qmd: Structural Basis of Selective Binding of Nonmethylated CpG Island... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qmd | ||||||
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Title | Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / CXXC-type Zn finger / DNA binding / unmethylated CpG motifs / nucleus speckle / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / cis-regulatory region sequence-specific DNA binding / methylated histone binding / nuclear matrix / nuclear speck / regulation of DNA-templated transcription ...unmethylated CpG binding / XBP1(S) activates chaperone genes / Set1C/COMPASS complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / cis-regulatory region sequence-specific DNA binding / methylated histone binding / nuclear matrix / nuclear speck / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Lam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat Commun / Year: 2011 Title: The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain. Authors: Xu, C. / Bian, C. / Lam, R. / Dong, A. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qmd.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qmd.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/3qmd ftp://data.pdbj.org/pub/pdb/validation_reports/qm/3qmd | HTTPS FTP |
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-Related structure data
Related structure data | 3qmbSC 3qmcC 3qmgC 3qmhC 3qmiC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9527.962 Da / Num. of mol.: 1 / Fragment: CXXC-type Zn finger Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXXC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9P0U4 | ||
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#2: DNA chain | Mass: 3672.406 Da / Num. of mol.: 1 / Fragment: DNA (Nonmethylated CpG Island) / Source method: obtained synthetically Details: DNA was purchased from Integrated DNA Technologies, Inc. | ||
#3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 1 / Fragment: DNA (Nonmethylated CpG Island) / Source method: obtained synthetically Details: DNA was purchased from Integrated DNA Technologies, Inc. | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes pH 7.5, 0.1M MgCl2, 30% PEG550MME., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010 Details: Rosenbaum-Rock high-resolution double-crystal monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 11621 / % possible obs: 97.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.067 / Χ2: 0.997 / Net I/σ(I): 12.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 33.79 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3QMB Resolution: 1.9→32.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.268 / WRfactor Rwork: 0.239 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.899 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.91 Å2 / Biso mean: 55.8028 Å2 / Biso min: 28.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.11 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: 20
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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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