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- PDB-5xew: Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xew | ||||||||||||||||||||||||||
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Title | Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex | ||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA/ANTIBIOTIC / Trinucleotide repeats / neurological disease / induced fit recognition / metal binding ligand / consecutive bases flip-out / DNA deformation / molecular diagnostics / DNA-ANTIBIOTIC complex | Function / homology | Chem-CPH / NICKEL (II) ION / DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Tseng, W.H. / Wu, P.C. / Hou, M.H. | ![]() ![]() Title: Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation Authors: Tseng, W.H. / Chang, C.K. / Wu, P.C. / Hu, N.J. / Lee, G.H. / Tzeng, C.C. / 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 | ![]() | 34.8 KB | Display | ![]() |
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PDB format | ![]() | 22.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Components
-DNA chain , 1 types, 2 molecules AB
#1: DNA chain | Mass: 3912.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 94 molecules ![](data/chem/img/CPH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | The force field of Chro unit used in the refinement of NiII(Chro)2-DNA complex structure was ...The force field of Chro unit used in the refinement of NiII(Chro)2-DNA complex structure was generated using the atomic resolution crystal structure of NiII(Chro)2. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.0 mM single stranded-DNA, 2.0 mM Chromomycin A3, 4mM NiSO4 6H2O, 50 mM sodium-cacodylate buffer, 5 mM MgCl2, 1 mM spermine, 3 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→30 Å / Num. obs: 21692 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 30.69 Å2 / Rmerge(I) obs: 0.05 / Χ2: 2.733 / Net I/σ(I): 28.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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 max: 115.53 Å2 / Biso mean: 39.6775 Å2 / Biso min: 20.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.751→23.192 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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