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- PDB-1u64: The Solution Structure of d(G3T4G4)2 -

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Entry
Database: PDB / ID: 1u64
TitleThe Solution Structure of d(G3T4G4)2
Components5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / G-quadruplex / monovalent cations
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsSket, P. / Crnugelj, M. / Plavec, J.
CitationJournal: Bioorg.Med.Chem. / Year: 2004
Title: d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH4+ ions.
Authors: Sket, P. / Crnugelj, M. / Plavec, J.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,9532
Polymers6,9532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 50structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #5fewest violations, lowest energy

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Components

#1: DNA chain 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
231PE-COSY
2412D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 4mM dG3T4G4 per strand; 90% H2O, 10% D2O, 15mM KCl; pH 5.5
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
115mM KCl 5.5ambient 278 K
215mM KCl 5.5ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
Felix2000Accelerysprocessing
Amber7Kollman, at allrefinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: 414 NOE-derived distance restraints associated with the nonexchangeable and exchangeable protons; 24 hydrogen-bond restraints; 66 torsion angle restraints for sugar moieties. For each of ...Details: 414 NOE-derived distance restraints associated with the nonexchangeable and exchangeable protons; 24 hydrogen-bond restraints; 66 torsion angle restraints for sugar moieties. For each of five different initial structures ten simulated annealing calculations at 700 K with NMR restraints using a generalized Born (GB) implicit solvation model were performed for 60 ps. The resulting structures were subjected to energy minimization
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 8

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