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BMRB: 16604

2KXM

1H, 13C, 15N chemical shift sssignments of the artificial neomycin-sensing riboswitch in complex with tobramycin

Authors

Schmidtke, S.R., Duchardt-Ferner, E., Weigand, J.E., Suess, B., Woehnert, J.

Assembly

rna-ligand complex

Entity

1. Neo-Riboswitch (polymer, Thiol state: not present), 27 monomers, 8620.002 Da Detail

GGCUGCUUGU CCUUUAAUGG UCCAGUC

2. TOY (non-polymer), 467.514 Da

Total weight

9087.516 Da

Max. entity weight

8620.002 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 77.8 %, Completeness: 9.3 %, Completeness (bb): 0.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	9.3 % (41 of 439)	11.2 % (27 of 240)	0.0 % (0 of 182)	82.4 % (14 of 17)
Suger, PO4	0.0 % (0 of 297)	0.0 % (0 of 162)	0.0 % (0 of 135)
Nucleobase	28.9 % (41 of 142)	34.6 % (27 of 78)	0.0 % (0 of 47)	82.4 % (14 of 17)
Aromatic	21.9 % (28 of 128)	21.9 % (14 of 64)	0.0 % (0 of 47)	82.4 % (14 of 17)

1. Neo-Riboswitch

GGCUGCUUGU CCUUUAAUGG UCCAGUC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	Neo-Aptamer	natural abundance	1.1 mM
2	Tobramycin	natural abundance	1.2 mM
3	potassium chloride	natural abundance	50 mM
4	potassium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
14	Tobramycin	natural abundance	1.2 mM
15	potassium chloride	natural abundance	50 mM
16	potassium phosphate	natural abundance	25 mM
17	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
18	Neo-Aptamer	[U-13C; U-15N]-Ura-Ade	1.2 mM
19	Tobramycin	natural abundance	1.3 mM
20	potassium chloride	natural abundance	50 mM
21	potassium phosphate	natural abundance	25 mM
22	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 47.0 %, Completeness (bb): 46.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	47.0 % (413 of 878)	46.9 % (225 of 480)	47.8 % (174 of 364)	41.2 % (14 of 34)
Suger, PO4	46.8 % (278 of 594)	46.6 % (151 of 324)	47.0 % (127 of 270)
Nucleobase	47.5 % (135 of 284)	47.4 % (74 of 156)	50.0 % (47 of 94)	41.2 % (14 of 34)
Aromatic	47.7 % (122 of 256)	47.7 % (61 of 128)	50.0 % (47 of 94)	41.2 % (14 of 34)

1. Neo-Riboswitch

GGCUGCUUGU CCUUUAAUGG UCCAGUC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	Neo-Aptamer	natural abundance	1.1 mM
2	Tobramycin	natural abundance	1.2 mM
3	potassium chloride	natural abundance	50 mM
4	potassium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
14	Tobramycin	natural abundance	1.2 mM
15	potassium chloride	natural abundance	50 mM
16	potassium phosphate	natural abundance	25 mM
17	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
18	Neo-Aptamer	[U-13C; U-15N]-Ura-Ade	1.2 mM
19	Tobramycin	natural abundance	1.3 mM
20	potassium chloride	natural abundance	50 mM
21	potassium phosphate	natural abundance	25 mM
22	D2O	natural abundance	100 %

Release date

2010-09-01

Citation

NMR resonance assignments of an engineered neomycin-sensing riboswitch RNA bound to ribostamycin and tobramycin
Schmidtke, S.R., Duchardt-Ferner, E., Weigand, J.E., Suess, B., Woehnert, J.
Biomol. NMR Assign. (2010), 4, 115-118, PubMed 20306311 , DOI 10.1007/s12104-010-9223-z , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 25526 released on 2016-01-31
    Title Re-refined solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostamycin complex
  BMRB: 16609 released on 2010-09-01
    Title 1H, 13C, 15N chemical shift sssignments of the artificial neomycin-sensing riboswitch in complex with ribostamycin

Related entities 1. Neo-Riboswitch, : 1 : 2 entities Detail

Experiments performed 16 experiments Detail

1 1D 1H-HS11ECHO

Instrument

Bruker Avance - 950 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	Neo-Aptamer	natural abundance	1.1 mM
2	Tobramycin	natural abundance	1.2 mM
3	potassium chloride	natural abundance	50 mM
4	potassium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	Neo-Aptamer	natural abundance	1.1 mM
2	Tobramycin	natural abundance	1.2 mM
3	potassium chloride	natural abundance	50 mM
4	potassium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 2D 1H-15N-HNN-COSY

Instrument

Bruker Avance - 800 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

5 2D 1H-13C-HNCO

Instrument

Bruker Avance - 800 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 2D 1H-13C H5(6)C5(6)C4N3H

Instrument

Bruker Avance - 700 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 2D 1H-15N HCN

Instrument

Bruker Avance - 600 MHz cryogenic probehead

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
14	Tobramycin	natural abundance	1.2 mM
15	potassium chloride	natural abundance	50 mM
16	potassium phosphate	natural abundance	25 mM
17	D2O	natural abundance	100 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz cryogenic probehead

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	Neo-Aptamer	[U-13C; U-15N]	1.1 mM
8	Tobramycin	natural abundance	1.2 mM
9	potassium chloride	natural abundance	50 mM
10	potassium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 2D 1H-13C HSQC