BMRB Entry 5717
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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/BMR5717
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Title: NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1
Deposition date: 2003-03-04 Original release date: 2003-04-30
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:
XBY6A, polymer, 14 residues, Formula weight is not available
XBY6B, 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):
XBY6A: CCAGGAGATTCCAC
XBY6B: GTGGAATCTCCTGG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 100 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | XBY6A | 1 |
| 2 | XBY6B | 2 |
Entities:
Entity 1, XBY6A 14 residues - Formula weight is not available
| 1 | DC | DC | DA | DG | DG | DA | DG | DA | DT | DT | ||||
| 2 | DC | DC | DA | DC |
Entity 2, XBY6B 14 residues - Formula weight is not available
| 1 | DG | DT | DG | DG | DA | DA | DT | DC | DT | DC | ||||
| 2 | DC | DT | DG | DG |
Samples:
sample_1: XBY6A0.5 – 1.0 mM; XBY6B0.5 – 1.0 mM
sample_2: XBY6A0.5 – 1.0 mM; XBY6B0.5 – 1.0 mM; Phosphate 20 mM; NaCl 56 mM; NaN3 50 mM; D2O 99.96%
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D NOESY | not available | not available | not available |
| 2D TOCSY | not available | not available | not available |
| 2D Exchange Spectroscopy | not available | not available | not available |
| 2D DQF-COSY | not available | not available | not available |
Software:
MORASS v2.5 - iterative matrix relaxation
AMBER v5 - molecular dynamics calculations
NMR spectrometers:
- Varian UNITYplus 600 MHz