9HRO | pdb_00009hro

Solution NMR structure of the synthetic tobramycin riboswitch in complex with tobramycin

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	1 mM unlabeled RNA (35-MER), 1.2 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE II 600
2	2D 1H-15N HSQC imino	0.5 mM [U-100% 15N] RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
3	2D 1H-15N HSQC amino	0.5 mM [U-100% 15N] RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE II 600
4	2D HNN-COSY	0.5 mM [U-100% 15N] RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
5	2D CPMG-NOESY	0.5 mM [U-100% 15N] RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
14	3D 1H-15N NOESY amino	0.5 mM [U-100% 15N] RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE III HD 700
13	2D long-range 1H-15N HSQC	0.5 mM [U-100% 15N] RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
17	2D 1H-13C HSQC aromatic	0.84 mM [U-13C; U-15N] RNA (35-MER), 1.004 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
16	2D 1H-13C HSQC aliphatic	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE III 950
15	2D H5(C5C4N4)H4	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE III HD 800
18	2D H1/H8-C5 HMBC	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
37	2D H(CC)H-TOCSY	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE NEO 600
19	2D H(N)CO	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE III HD 800
20	2D H(C)N aromatic	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 700
21	2D H(C)N aromatic	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE NEO 600
22	2D H(C)N aliphatic	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 700
23	2D H(C)N aliphatic	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE NEO 600
24	3D 1H-13C NOESY-HSQC aro	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III 950
25	3D 1H-13C NOESY-HSQC ali	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 800
26	3D 1H-13C NOESY-HSQC ali	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III 950
27	3D HCCH-COSY	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 800
28	3D HCCH-COSY	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 800
29	3D HCCH-TOCSY	0.5 mM [U-13C; U-15N]-Ura,Gua RNA (35-MER), 0.6 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 800
30	3D HCCH-TOCSY	0.75 mM [U-13C; U-15N]-Ade,Cyt RNA (35-MER), 0.9 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 800
31	2D f1-filtered 1H-1H TOCSY	0.84 mM [U-13C; U-15N] RNA (35-MER), 1.004 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
32	2D fi1-filtered 1H-1H TOCSY	0.84 mM [U-13C; U-15N] RNA (35-MER), 1.004 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE II 600
34	2D 1H-1H TOCSY	1 mM [U-100% 2H] RNA (35-MER), 1.2 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE II 600
35	2D 1H-1H TOCSY	1 mM [U-100% 2H] RNA (35-MER), 1.2 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE II 600
33	2D f1,f2-filtered 1H-1H NOESY	0.84 mM [U-13C; U-15N] RNA (35-MER), 1.004 mM unlabeled TOBRAMYCIN	95% H2O/5% D2O	85.9 M	6.2	1 bar	283	Bruker AVANCE NEO 600
36	3D HCP	2.8 mM [U-13C; U-15N]-Ura RNA (35-MER), 2.2 mM unlabeled TOBRAMYCIN	100% D2O	85.9 M	6.2	1 bar	298	Bruker AVANCE III HD 700

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

NMR Refinement
Method	Details	Software
distance geometry		CYANA

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	TopSpin		Bruker Biospin
3	chemical shift assignment	CARA		Keller and Wuthrich
4	peak picking	CARA		Keller and Wuthrich
5	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
6	refinement	CYANA		Guntert, Mumenthaler and Wuthrich