2KXM

Solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostmycin complex

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.8 mM RNA (27-MER)-1, 25 mM potassium phosphate-2, 50 mM potassium chloride-3	90% H2O/10% D2O		6.2		267-298
2	2D 1H-15N HSQC	0.8 mM [U-100% 15N] RNA (27-MER)-4, 0.9 mM RIBOSTAMYCIN-5, 25 mM potassium phosphate-6, 50 mM potassium chloride-7	90% H2O/10% D2O		6.2		283
3	3D 1H-15N NOESY	0.8 mM [U-100% 15N] RNA (27-MER)-4, 0.9 mM RIBOSTAMYCIN-5, 25 mM potassium phosphate-6, 50 mM potassium chloride-7	90% H2O/10% D2O		6.2		283
4	2D 1H-13C HSQC	1.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-8, 1.2 mM RIBOSTAMYCIN-9, 25 mM potassium phosphate-10, 50 mM potassium chloride-11	100% D2O		6.2		298
5	3D HNCO	1.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-16, 1.2 mM RIBOSTAMYCIN-17, 25 mM potassium phosphate-18, 50 mM potassium chloride-19	90% H2O/10% D2O		6.2		283
6	3D H(CCO)NH	1.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-16, 1.2 mM RIBOSTAMYCIN-17, 25 mM potassium phosphate-18, 50 mM potassium chloride-19	90% H2O/10% D2O		6.2		283
7	3D 1H-13C NOESY	1.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-8, 1.2 mM RIBOSTAMYCIN-9, 25 mM potassium phosphate-10, 50 mM potassium chloride-11	100% D2O		6.2		298
8	3D 1H-13C NOESY	1.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-8, 1.2 mM RIBOSTAMYCIN-9, 25 mM potassium phosphate-10, 50 mM potassium chloride-11	100% D2O		6.2		298
9	2D 1H-1H TOCSY	1.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-12, 1.2 mM RIBOSTAMYCIN-13, 25 mM potassium phosphate-14, 50 mM potassium chloride-15	100% D2O		6.2		298
10	2D DQF-COSY	1.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-12, 1.2 mM RIBOSTAMYCIN-13, 25 mM potassium phosphate-14, 50 mM potassium chloride-15	100% D2O		6.2		298
11	2D 1H-1H NOESY	1.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-12, 1.2 mM RIBOSTAMYCIN-13, 25 mM potassium phosphate-14, 50 mM potassium chloride-15	100% D2O		6.2		298
12	2D 1H-1H TOCSY	1.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-20, 1.2 mM RIBOSTAMYCIN-21, 25 mM potassium phosphate-22, 50 mM potassium chloride-23	90% H2O/10% D2O		6.2		283
13	2D 1H-1H NOESY	1.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-20, 1.2 mM RIBOSTAMYCIN-21, 25 mM potassium phosphate-22, 50 mM potassium chloride-23	90% H2O/10% D2O		6.2		283

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	700
3	Bruker	AVANCE	800
4	Bruker	AVANCE	900
5	Bruker	AVANCE	950

NMR Refinement
Method	Details	Software
DGSA-distance geometry simulated annealing		TopSpin

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	2.1	Bruker Biospin
2	processing	TopSpin	2.1	Bruker Biospin
3	chemical shift assignment	CARA	1.8.4.2	Wuthrich
4	peak picking	CARA	1.8.4.2	Wuthrich
5	chemical shift assignment	Sparky		Goddard
6	peak picking	Sparky		Goddard
7	structure solution	CYANA		Guntert, Mumenthaler and Wuthrich
8	refinement	OPAL		Luginbuhl, Guntert, Billeter, Wuthrich

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.