BMRB Entry 5718

Name: Chemical Shifts for the XBY2 DNA Duplex
Published: 2003-04-30

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PDB ID: 1k8j
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR5718
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Chemical Shifts for the XBY2 DNA Duplex

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:

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:

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

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1
- chemical_shift_set_2

Data type	Count
1H chemical shifts	198

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	XBY2A	1
2	XBY2B	2

Entities:

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

1

DC

DA

DG

DA

DG

DA

DT

2

DC

DA

DC

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

1

DG

DT

DG

DA

DT

DC

DT

DC

2

DC

DT

DG

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:

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