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Open data
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Basic information
Entry | Database: PDB / ID: 5zt2 | |||||||||||||||||||||||
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Title | Crystal structure of CCG DNA repeats at 1.66 angstrom resolution | |||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / DNA structures / i-motifs / neurological disease / tetraplex structures | Function / homology | : / DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hou, M.H. / Wu, P.C. / Satange, R.B. / Chen, Y.W. | ![]() ![]() Title: Crystallographic analysis of conformational change in CCG repeats into i-motif and unusual DNA duplex in presence and absence of CoII(Chro)2 complex Authors: Hou, M.H. #1: ![]() Title: Structural basis for the identification of an i-motif tetraplex core with a parallel-duplex junction as a structural motif in CCG triplet repeats. Authors: Chen, Y.W. / Jhan, C.R. / Neidle, S. / Hou, M.H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.3 KB | Display | ![]() |
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PDB format | ![]() | 15 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 345.7 KB | Display | ![]() |
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Full document | ![]() | 345.7 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3295.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50mM Sodium cacodylate, 1mM Magnesium chloride, 5% MPD, 2mM Cobalt(II) chloride, 1mM Chromomycin A3 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 18, 2013 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.66→30 Å / Num. obs: 3447 / % possible obs: 96.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.5972142739 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 41.724 | ||||||||||||
Reflection shell | Resolution: 1.66→1.72 Å / Rmerge(I) obs: 0.272 / Num. unique obs: 632 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7353127997 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66002164937→12.4437277752 Å
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Refine LS restraints |
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LS refinement shell |
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