2MIY | pdb_00002miy

Solution NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	1.2 mM RNA (59-MER), 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 60 mM potassium chloride, 3 mM calcium chloride	90% H2O/10% D2O	66	6-6.3	ambient	300
2	2D 1H-1H TOCSY	1.2 mM RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	300
3	3D HCCH-TOCSY	1.2 mM [U-13C; U-15N]-Ade RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	310
4	3D HCCH-TOCSY	1.2 mM [U-13C; U-15N]-Gua RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	310
5	3D HCCH-TOCSY	1.2 mM [U-13C; U-15N]-Cyt RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	310
6	3D HCCH-TOCSY	1.2 mM [U-13C; U-15N]-Ura RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	310
7	2D 1H-1H NOESY	1 mM (U-50%)-2H RNA (59-MER), 60 mM potassium chloride, 3 mM calcium Chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	300
8	2D 1H-1H NOESY	1.2 mM RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	100% D2O	66	6-6.3	ambient	300
9	2D 1H-13C HSQC	1.2 mM [U-100% 13C; U-100% 15N] RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	90% H2O/10% D2O	66	6-6.3	ambient	300
10	2D 1H-15N HSQC	1.2 mM [U-100% 13C; U-100% 15N] RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE	90% H2O/10% D2O	66	6-6.3	ambient	300

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600
2	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing		Sparky

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	18
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	Sparky		Goddard
2	chemical shift assignment	Sparky		Goddard
3	collection	XwinNMR		Bruker Biospin
4	processing	XwinNMR		Bruker Biospin
5	collection	TopSpin		Bruker Biospin
6	processing	TopSpin		Bruker Biospin
7	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
8	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
9	peak picking	NMRDraw		Johnson, One Moon Scientific
10	data analysis	Insight II		Accelrys Software Inc.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.