BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 5718

Title: Chemical Shifts for the XBY2 DNA Duplex

Authors: Volk, D.; Yang, X.; Fennewald, S.; King, D.; Bassett, Suzanne; Venkitachalam, S.; Herzog, N.; Luxon, B.; Gorenstein, D.

Citation: Volk, David; Yang, Xianbin; Fennewald, Susan; King, David; Bassett, Suzanne; Venkitachalam, Sheela; Herzog, Norbert; Luxon, Bruce; Gorenstein, David. "Solution Structure and Design of Dithiophosphate Backbone Aptamers Targeting Transcription Factor NF-kB"  Bioorg. Chem. 30, 396-419 (2002).

Assembly members:
XBY2A, polymer, 14 residues, Formula weight is not available
XBY2B, polymer, 14 residues, Formula weight is not available

Natural source:   Common Name: E. Coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
XBY2A: CCAGGAGATTCCAC
XBY2B: GTGGAATCTCCTGG

Data sets:
Data typeCount
1H chemical shifts198

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1XBY2A1
2XBY2B2

Entities:

Entity 1, XBY2A 14 residues - Formula weight is not available

1   DCDCDADGDGDADGDADTDT
2   DCDCDADC

Entity 2, XBY2B 14 residues - Formula weight is not available

1   DGDTDGDGDADADTDCDTDC
2   DCDTDGDG

Samples:

sample_1: XBY2A0.5 – 1.0 mM; XBY2B0.5 – 1.0 mM; Phosphate 20 mM; NaCl 56 mM; NaN3 50 mM; D2O 99.96%

sample_2: XBY2A0.5 – 1.0 mM; XBY2B0.5 – 1.0 mM

sample_cond_1: pH: 6.7; temperature: 278 K; ionic strength: 100 mM; pressure: 1 atm

sample_cond_2: pH: 6.7; temperature: 288 K; ionic strength: 100 mM; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
2D NOESYnot availablenot availablenot available
2D TOCSYnot availablenot availablenot available
2D Exchange Spectroscopynot availablenot availablenot available
2D DQF-COSYnot availablenot availablenot available

Software:

MORASS v2.5 - iterative matrix relaxation

AMBER v5 - molecular dynamics calculations

NMR spectrometers:

  • Varian UNITYplus 600 MHz

Related Database Links: