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- PDB-4da3: Crystal structure of an intramolecular human telomeric DNA G-quad... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4da3 | ||||||||||||||||||||
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Title | Crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41. | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / intramolecular / ligand-complex / G-quadruplex / telomere | Function / homology | Chem-0DX / : / DNA / DNA (> 10) | ![]() Biological species | Synthetic DNA (others) | Method | ![]() ![]() ![]() ![]() Collie, G.W. / Neidle, S. | ![]() ![]() Title: Structure-based design and evaluation of naphthalene diimide g-quadruplex ligands as telomere targeting agents in pancreatic cancer cells. Authors: Micco, M. / Collie, G.W. / Dale, A.G. / Ohnmacht, S.A. / Pazitna, I. / Gunaratnam, M. / Reszka, A.P. / Neidle, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.6 KB | Display | ![]() |
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PDB format | ![]() | 16.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3uyhC ![]() 4daqC ![]() 3sc8S C: citing same article ( S: Starting model for refinement |
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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: 6670.290 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: DNA synthesized by standard phosphoramidite chemistry. Source: (synth.) Synthetic DNA (others) | ||||
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#2: Chemical | #3: Chemical | ChemComp-0DX / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG400, 150 mM sodium chloride and 50 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→25.97 Å / Num. all: 3843 / Num. obs: 3843 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 66.213 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.27→2.33 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique all: 278 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SC8 Resolution: 2.4→14.81 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.523 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→14.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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