2MXS | pdb_00002mxs

Solution NMR-structure of the neomycin sensing riboswitch RNA bound to paromomycin

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.64 mM RNA (27-MER), 0.64 mM Paromomycin	90% H2O/10% D2O		6.2	ambient	283
2	2D 1H-15N HSQC	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	90% H2O/10% D2O		6.2	ambient	283
3	2D 1H-13C HNCO	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	90% H2O/10% D2O		6.2	ambient	283
4	2D 1H-15N H56C56C4N3H	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	90% H2O/10% D2O		6.2	ambient	283
5	2D 1H-15N HSQC NH2 only	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	90% H2O/10% D2O		6.2	ambient	283
6	2D 1H-13C HSQC aromatic	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
7	2D 1H-13C HSQC aliphatic	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
8	2D 1H-13C HSQC aliphatic	0.62 mM G-]13C; 15N] RNA (27-MER), 0.62 mM Paromomycin	100% D2O		6.2	ambient	298
9	3D 1H-13C NOESY-HSQC aliphatic	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
10	3D 1H-13C NOESY-HMQC aromatic	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
11	3D HCCH-COSY	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
12	3D HCCH-TOCSY	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
13	2D 1H-15N lrHSQC	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
14	2D DQF-COSY	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
15	2D 1H-31P HCP	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
16	3D HCCH-TOCSY-E.COSY	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
17	2D 13C filter NOESY	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
18	2D 13C filter TOCSY	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
19	2D quant 31P coupled 1H, 13C HSQC	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298
20	2D quant 31P coupled 1H-13C HMQC	0.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin	100% D2O		6.2	ambient	298

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

NMR Refinement
Method	Details	Software
torsion angle dynamics, energy minimization		TopSpin

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

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