+Open data
-Basic information
Entry | Database: PDB / ID: 1lvs | ||||||||||||||||||
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Title | THE SOLUTION STRUCTURE OF D(G4T4G3)2 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / G-quartet / cation coordination / telomeric repeat | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, molecular dynamics | Authors | Crnugelj, M. / Hud, N.V. / Plavec, J. | Citation | Journal: J.Mol.Biol. / Year: 2002 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lvs.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lvs.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lvs_validation.pdf.gz | 311.8 KB | Display | wwPDB validaton report |
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Full document | 1lvs_full_validation.pdf.gz | 409.3 KB | Display | |
Data in XML | 1lvs_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1lvs_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lvs ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lvs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-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: simulated annealing, molecular dynamics / Software ordinal: 1 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 |