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- PDB-2akg: Thallium form of the G-Quadruplex from Oxytricha Nova, d(G4T4G4)2 -

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Basic information

Entry
Database: PDB / ID: 2akg
TitleThallium form of the G-Quadruplex from Oxytricha Nova, d(G4T4G4)2
Components5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / Deoxyribonucleic acid / G-Quadruplex / Thallium
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) restrained molecular dynamics (100 cycles of 200 steps each)
AuthorsGill, M.L. / Strobel, S.A. / Loria, J.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: (205)Tl NMR methods for the characterization of monovalent cation binding to nucleic acids
Authors: Gill, M.L. / Strobel, S.A. / Loria, J.P.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 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*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,6112
Polymers7,6112
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Sequence obtained from Sterkiella nova (Oxytricha nova) telomere

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
13131P-1H COSY
2422D NOESY
NMR detailsText: This structure was determined without the use of isotopically enriched nucleotides.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0, 100% D2O100% D2O
20.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0, 90% H2O/10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.51 atm298 K
26.51 atm278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVarian, Inccollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
Sparky3.11Goddard and Knellerdata analysis
CNS1.1Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warreniterative matrix relaxation
CNS1.1Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenrefinement
CNS1.1Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure solution
RefinementMethod: (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) ...Method: (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) restrained molecular dynamics (100 cycles of 200 steps each)
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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