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Open data
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Basic information
Entry | Database: PDB / ID: 1lvs | ||||||||||||||||||
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Title | THE SOLUTION STRUCTURE OF D(G4T4G3)2 | ||||||||||||||||||
![]() | 5'-D(*![]() ![]() Function / homology | ![]() ![]() Method | ![]() ![]() ![]() ![]() Crnugelj, M. / Hud, N.V. / Plavec, J. | ![]() ![]() Title: The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold. Authors: Crnugelj, M. / Hud, N.V. / Plavec, 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 | ![]() | 141.7 KB | Display | ![]() |
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PDB format | ![]() | 116.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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NMR ensembles |
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Components
#1: DNA chain | Mass: 3476.254 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Oligomer has been prepared on solid state support using phosphoramidite chemistry. |
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-Experimental details
-Experiment
Experiment | Method: ![]() | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
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Sample preparation
Details | Contents: 5 mM dG4T4G3 per strand; 90%H2O, 10% D2O; 50 mM NaCl; pH 7.2 Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample conditions |
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Crystal grow![]() | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: ![]() ![]() Details: 517 NOE-derived distance restraints associated with the nonexchangeable and exchangeable protons; 24 hydrogen-bond restraints; 95 torsion angle restraints for sugar moieties. Thirty 250 ps ...Details: 517 NOE-derived distance restraints associated with the nonexchangeable and exchangeable protons; 24 hydrogen-bond restraints; 95 torsion angle restraints for sugar moieties. Thirty 250 ps simulated annealing calculations at 800 K were initially performed. Further refinement via solvated MD simulations (750ps, TIP3P water, particle mesh Ewald method) followed by energy minimization. | ||||||||||||||||
NMR representative | Selection criteria: fewest violations, lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 10 |