BMRB Entry 34386

Title:
SC14 G-hairpin
Deposition date:
2019-04-01
Original release date:
2021-02-01
Authors:
Lenarcic Zivkovic, M.; Trantirek, L.; Plavec, J.
Citation:

Citation: Zdivkovic, Martina Lenarcic; Gajarsky, Martin; Bekova, Katerina; Stadlbauer, Petr; Vicherek, Lukas; Petrova, Magdalena; Fiala, Radovan; Rosenberg, Ivan; Sponer, Jiri; Plavec, Janez; Trantirek, Lukas. "Insight into formation propensity of pseudocircular DNA G-hairpins"  Nucleic Acids Res. 49, 2317-2332 (2021).
PubMed: 33524154

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 4413.846 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTGTGTGGGTGTGT

Data sets:
Data typeCount
1H chemical shifts135

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 14 residues - 4413.846 Da.

1   DGDTDGDTDGDTDGDGDGDT
2   DGDTDGDT

Samples:

sample_1: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3') 0.6 mM

sample_2: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3') 0.6 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 120 mM; pH: 7.0 pD; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D NOESYsample_2isotropicsample_conditions_2
2D TOCSYsample_2isotropicsample_conditions_2
2D DQF COSYsample_2isotropicsample_conditions_2
1D 15N-edited HSQCsample_1isotropicsample_conditions_1
2D NOESYsample_1isotropicsample_conditions_1
2D NOESYsample_2isotropicsample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment

AMBER14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

VNMR, Varian - processing

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

  • Bruker AvanceIII 700 MHz
  • Bruker AvanceIII 850 MHz
  • Agilent DD2 600 MHz
  • Bruker AvanceIII 950 MHz
  • Bruker AvanceIII 600 MHz