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BMRB: 25427

2MXS

DNA/RNA (28-MER)

Authors

Schmidtke, S., Duchardt-Ferner, E., Ohlenschlaeger, O., Gottstein, D., Wohnert, J.

Assembly

DNA/RNA (28-MER)

Entity

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

GGCUGCUUGU CCUUUAAUGG UCCAGUC

2. PAROMOMYCIN (non-polymer), 615.628 Da

Total weight

9235.63 Da

Max. entity weight

8620.002 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 51.3 %, Completeness (bb): 31.6 % Detail

Polymer type: DNA/RNA hybrid

	Total	¹H	¹³C	¹⁵N
All	51.3 % (225 of 439)	57.5 % (138 of 240)	40.7 % (74 of 182)	76.5 % (13 of 17)
Suger, PO4	31.6 % (94 of 297)	40.7 % (66 of 162)	20.7 % (28 of 135)
Nucleobase	92.3 % (131 of 142)	92.3 % (72 of 78)	97.9 % (46 of 47)	76.5 % (13 of 17)
Aromatic	93.0 % (119 of 128)	93.8 % (60 of 64)	97.9 % (46 of 47)	76.5 % (13 of 17)

1. RNA (27-MER)

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	RNA (27-MER)	natural abundance	0.64 mM
2	Paromomycin	natural abundance	0.64 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

Sample #3

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

#	Name	Isotope labeling	Concentration
9	RNA (27-MER)	13C; 15N	0.89 mM
10	Paromomycin	natural abundance	0.89 mM
11	D2O	natural abundance	100 %

Sample #4

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

#	Name	Isotope labeling	Concentration
12	RNA (27-MER)	G-]13C; 15N]	0.62 mM
13	Paromomycin	natural abundance	0.62 mM
14	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 65.4 %, Completeness (bb): 58.6 % Detail

Polymer type: DNA/RNA hybrid

	Total	¹H	¹³C	¹⁵N
All	65.4 % (574 of 878)	65.8 % (316 of 480)	67.0 % (244 of 364)	41.2 % (14 of 34)
Suger, PO4	58.6 % (348 of 594)	60.8 % (197 of 324)	55.9 % (151 of 270)
Nucleobase	79.6 % (226 of 284)	76.3 % (119 of 156)	98.9 % (93 of 94)	41.2 % (14 of 34)
Aromatic	83.6 % (214 of 256)	83.6 % (107 of 128)	98.9 % (93 of 94)	41.2 % (14 of 34)

1. RNA (27-MER)

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	RNA (27-MER)	natural abundance	0.64 mM
2	Paromomycin	natural abundance	0.64 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

Sample #3

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

#	Name	Isotope labeling	Concentration
9	RNA (27-MER)	13C; 15N	0.89 mM
10	Paromomycin	natural abundance	0.89 mM
11	D2O	natural abundance	100 %

Sample #4

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

#	Name	Isotope labeling	Concentration
12	RNA (27-MER)	G-]13C; 15N]	0.62 mM
13	Paromomycin	natural abundance	0.62 mM
14	D2O	natural abundance	100 %

Chem. Shift Complete3

Sequence coverage: 3.7 %, Completeness: 43.7 %, Completeness (bb): 39.1 % Detail

Polymer type: DNA/RNA hybrid

	Total	¹H	¹³C	¹⁵N
All	43.7 % (576 of 1317)	44.0 % (317 of 720)	44.7 % (244 of 546)	29.4 % (15 of 51)
Suger, PO4	39.1 % (348 of 891)	40.5 % (197 of 486)	37.3 % (151 of 405)
Nucleobase	53.5 % (228 of 426)	51.3 % (120 of 234)	66.0 % (93 of 141)	29.4 % (15 of 51)
Aromatic	56.3 % (216 of 384)	56.3 % (108 of 192)	66.0 % (93 of 141)	29.4 % (15 of 51)

1. RNA (27-MER)

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	RNA (27-MER)	natural abundance	0.64 mM
2	Paromomycin	natural abundance	0.64 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

Sample #3

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

#	Name	Isotope labeling	Concentration
9	RNA (27-MER)	13C; 15N	0.89 mM
10	Paromomycin	natural abundance	0.89 mM
11	D2O	natural abundance	100 %

Sample #4

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

#	Name	Isotope labeling	Concentration
12	RNA (27-MER)	G-]13C; 15N]	0.62 mM
13	Paromomycin	natural abundance	0.62 mM
14	D2O	natural abundance	100 %

Chem. Shift Complete4

Sequence coverage: 0.0 %, Completeness: 32.8 %, Completeness (bb): 29.3 % Detail

Polymer type: DNA/RNA hybrid

	Total	¹H	¹³C	¹⁵N
All	32.8 % (576 of 1756)	33.0 % (317 of 960)	33.5 % (244 of 728)	22.1 % (15 of 68)
Suger, PO4	29.3 % (348 of 1188)	30.4 % (197 of 648)	28.0 % (151 of 540)
Nucleobase	40.1 % (228 of 568)	38.5 % (120 of 312)	49.5 % (93 of 188)	22.1 % (15 of 68)
Aromatic	42.2 % (216 of 512)	42.2 % (108 of 256)	49.5 % (93 of 188)	22.1 % (15 of 68)

1. RNA (27-MER)

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	RNA (27-MER)	natural abundance	0.64 mM
2	Paromomycin	natural abundance	0.64 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

Sample #3

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

#	Name	Isotope labeling	Concentration
9	RNA (27-MER)	13C; 15N	0.89 mM
10	Paromomycin	natural abundance	0.89 mM
11	D2O	natural abundance	100 %

Sample #4

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

#	Name	Isotope labeling	Concentration
12	RNA (27-MER)	G-]13C; 15N]	0.62 mM
13	Paromomycin	natural abundance	0.62 mM
14	D2O	natural abundance	100 %

Chem. Shift Complete5

Sequence coverage: 100.0 %, Completeness: 42.4 %, Completeness (bb): 41.0 % Detail

Polymer type: DNA/RNA hybrid

	Total	¹H	¹³C	¹⁵N
All	42.4 % (931 of 2195)	41.6 % (499 of 1200)	45.8 % (417 of 910)	17.6 % (15 of 85)
Suger, PO4	41.0 % (609 of 1485)	41.0 % (332 of 810)	41.0 % (277 of 675)
Nucleobase	45.4 % (322 of 710)	42.8 % (167 of 390)	59.6 % (140 of 235)	17.6 % (15 of 85)
Aromatic	48.4 % (310 of 640)	48.4 % (155 of 320)	59.6 % (140 of 235)	17.6 % (15 of 85)

1. RNA (27-MER)

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	RNA (27-MER)	natural abundance	0.64 mM
2	Paromomycin	natural abundance	0.64 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

Sample #3

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

#	Name	Isotope labeling	Concentration
9	RNA (27-MER)	13C; 15N	0.89 mM
10	Paromomycin	natural abundance	0.89 mM
11	D2O	natural abundance	100 %

Sample #4

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

#	Name	Isotope labeling	Concentration
12	RNA (27-MER)	G-]13C; 15N]	0.62 mM
13	Paromomycin	natural abundance	0.62 mM
14	D2O	natural abundance	100 %

Release date

2015-12-06

Citation

What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch
Duchardt-Ferner, E., Schmidtke, S., Weigand, J., Ohlenschlaeger, O., Wurm, J., Hammann, C., Suess, B., Wohnert, J.
Angew. Chem Int Ed Engl. (2015), 55, 1527-1530, PubMed 26661511 , DOI 10.1002/anie.201507365 , Abstract

Related entities 1. RNA (27-MER), : 1 : 2 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	RNA (27-MER)	natural abundance	0.64 mM
2	Paromomycin	natural abundance	0.64 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

3 2D 1H-13C HNCO

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

4 2D 1H-15N H56C56C4N3H

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

5 2D 1H-15N HSQC NH2 only

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Concentration
5	RNA (27-MER)	13C; 15N	0.89 mM
6	Paromomycin	natural abundance	0.89 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %

6 2D 1H-13C HSQC aromatic