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- PDB-3qmi: Structural Basis of Selective Binding of Non-Methylated CpG islan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qmi | ||||||
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Title | Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-ACGT) by the CXXC Domain of CFP1 | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / DNA BINDING / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, C. / Bian, C. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.6 KB | Display | ![]() |
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PDB format | ![]() | 25.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qmbSC ![]() 3qmcC ![]() 3qmdC ![]() 3qmgC ![]() 3qmhC 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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Unit cell |
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Components
-Protein / DNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 9527.962 Da / Num. of mol.: 1 / Fragment: CXXC-type Zn finger, residues 161-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Fragment: DNA (nonmethylated CpG island) / Source method: obtained synthetically |
-Non-polymers , 4 types, 38 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.65 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 8362 |
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Processing
Software | Name: REFMAC / Version: 5.5.0110 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 3QMB Resolution: 2.1→37.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.463 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / 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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