BMRB Entry 19158

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19158
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Title:
Solution NMR structure of the d(GGGTTGGGTTTTGGGTGGG) quadruplex in sodium conditions
Deposition date:
2013-04-10
Original release date:
2014-04-16
Authors:
Karsisiotis, Andreas Ioannis; Webba da Silva, Mateus
Citation:

Citation: Karsisiotis, Andreas Ioannis; Webba da Silva, Christopher. "DNA quadruplex folding formalism--a tutorial on quadruplex topologies."  Methods 64, 28-35 (2013).
PubMed: 23791747

Assembly members:

Assembly members:
DNA_(5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'), polymer, 19 residues, 6034.914 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: obtained from a vendor

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3'): GGGTTGGGTTTTGGGTGGG

Data typeCount
1H chemical shifts349
31P chemical shifts18

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3')1

Entities:

Entity 1, DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3') 19 residues - 6034.914 Da.

1   DGDGDGDTDTDGDGDGDTDT
2   DTDTDGDGDGDTDGDGDG

Samples:

S026_(H2O): DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3')4 – 6 mM; sodium phosphate 20 mM

S026_(D2O): DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3')4 – 6 mM; sodium phosphate 20 mM

Exchangeable_protons_278K: ionic strength: 25 mM; pH: 7.8; pressure: 1 atm; temperature: 278 K

Non_exchangeable_protons_293K: ionic strength: 25 mM; pH: 7.8; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYS026_(H2O)isotropicExchangeable_protons_278K
2D 1H-1H NOESYS026_(D2O)isotropicNon_exchangeable_protons_293K
2D 1H-1H TOCSYS026_(D2O)isotropicNon_exchangeable_protons_293K
2D DQF-COSYS026_(D2O)isotropicNon_exchangeable_protons_293K
2D [1H-13C] H1(C5)H8 JR HMBCS026_(H2O)isotropicExchangeable_protons_278K
2D [1H-31P]-HSQCS026_(D2O)isotropicNon_exchangeable_protons_293K

Software:

FELIX, Accelrys Software Inc. - processing

SPARKY, Goddard - chemical shift assignment, data analysis

X-PLOR, Brunger - refinement, structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

VNMRJ, Varian - collection

NMR spectrometers:

  • Varian VNMRS 500 500 MHz