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BMRB: 19039

2M57

NMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8

Authors

Pechlaner, M., Donghi, D., Zelenay, V., Sigel, R.K. O.

Assembly

domain 5 from Azotobacter vinelandii Intron 5

Entity

1. domain 5 from Azotobacter vinelandii Intron 5 (polymer, Thiol state: not present), 35 monomers, 11331.68 Da Detail

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Formula weight

11331.68 Da

Source organism

Azotobacter vinelandii

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 29.5 %, Completeness (bb): 17.7 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	29.5 % (165 of 559)	41.2 % (126 of 306)	16.7 % (39 of 233)	0.0 % (0 of 20)
Suger, PO4	17.7 % (68 of 385)	32.4 % (68 of 210)	0.0 % (0 of 175)
Nucleobase	55.7 % (97 of 174)	60.4 % (58 of 96)	67.2 % (39 of 58)	0.0 % (0 of 20)
Aromatic	62.2 % (97 of 156)	74.4 % (58 of 78)	67.2 % (39 of 58)	0.0 % (0 of 20)

1. RNA (35-MER)

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
1	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	60 mM
3	EDTA	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
4	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
5	potassium chloride	natural abundance	60 mM
6	EDTA	natural abundance	10 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
7	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
8	potassium chloride	natural abundance	60 mM
9	EDTA	natural abundance	10 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
10	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
11	potassium chloride	natural abundance	60 mM
12	EDTA	natural abundance	10 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
13	RNA (35-MER)	[3',4',5',5'',5]-100% 2D	0.5 ~ 1.0 mM
14	potassium chloride	natural abundance	60 mM
15	EDTA	natural abundance	10 uM

Chem. Shift Complete2

Sequence coverage: 91.4 %, Completeness: 26.7 %, Completeness (bb): 16.4 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	26.7 % (298 of 1118)	37.3 % (228 of 612)	15.0 % (70 of 466)	0.0 % (0 of 40)
Suger, PO4	16.4 % (126 of 770)	30.0 % (126 of 420)	0.0 % (0 of 350)
Nucleobase	49.4 % (172 of 348)	53.1 % (102 of 192)	60.3 % (70 of 116)	0.0 % (0 of 40)
Aromatic	55.1 % (172 of 312)	65.4 % (102 of 156)	60.3 % (70 of 116)	0.0 % (0 of 40)

1. RNA (35-MER)

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
1	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	60 mM
3	EDTA	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
4	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
5	potassium chloride	natural abundance	60 mM
6	EDTA	natural abundance	10 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
7	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
8	potassium chloride	natural abundance	60 mM
9	EDTA	natural abundance	10 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
10	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
11	potassium chloride	natural abundance	60 mM
12	EDTA	natural abundance	10 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
13	RNA (35-MER)	[3',4',5',5'',5]-100% 2D	0.5 ~ 1.0 mM
14	potassium chloride	natural abundance	60 mM
15	EDTA	natural abundance	10 uM

Chem. Shift Complete3

Sequence coverage: 97.1 %, Completeness: 39.7 %, Completeness (bb): 33.6 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	39.7 % (666 of 1677)	49.0 % (450 of 918)	30.9 % (216 of 699)	0.0 % (0 of 60)
Suger, PO4	33.6 % (388 of 1155)	46.8 % (295 of 630)	17.7 % (93 of 525)
Nucleobase	53.3 % (278 of 522)	53.8 % (155 of 288)	70.7 % (123 of 174)	0.0 % (0 of 60)
Aromatic	59.4 % (278 of 468)	66.2 % (155 of 234)	70.7 % (123 of 174)	0.0 % (0 of 60)

1. RNA (35-MER)

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
1	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	60 mM
3	EDTA	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
4	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
5	potassium chloride	natural abundance	60 mM
6	EDTA	natural abundance	10 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
7	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
8	potassium chloride	natural abundance	60 mM
9	EDTA	natural abundance	10 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
10	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
11	potassium chloride	natural abundance	60 mM
12	EDTA	natural abundance	10 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K

#	Name	Isotope labeling	Concentration
13	RNA (35-MER)	[3',4',5',5'',5]-100% 2D	0.5 ~ 1.0 mM
14	potassium chloride	natural abundance	60 mM
15	EDTA	natural abundance	10 uM

Chem. Shift Complete4

Sequence coverage: 68.6 %, Completeness: 31.8 %, Completeness (bb): 25.2 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	31.8 % (712 of 2236)	39.4 % (482 of 1224)	23.2 % (216 of 932)	17.5 % (14 of 80)
Suger, PO4	25.2 % (388 of 1540)	35.1 % (295 of 840)	13.3 % (93 of 700)
Nucleobase	46.6 % (324 of 696)	48.7 % (187 of 384)	53.0 % (123 of 232)	17.5 % (14 of 80)
Aromatic	49.4 % (308 of 624)	54.8 % (171 of 312)	53.0 % (123 of 232)	17.5 % (14 of 80)

1. RNA (35-MER)

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 7.8

#	Name	Isotope labeling	Concentration
1	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	60 mM
3	EDTA	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 7.8

#	Name	Isotope labeling	Concentration
4	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
5	potassium chloride	natural abundance	60 mM
6	EDTA	natural abundance	10 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 7.8

#	Name	Isotope labeling	Concentration
7	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
8	potassium chloride	natural abundance	60 mM
9	EDTA	natural abundance	10 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 7.8

#	Name	Isotope labeling	Concentration
10	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
11	potassium chloride	natural abundance	60 mM
12	EDTA	natural abundance	10 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 7.8

#	Name	Isotope labeling	Concentration
13	RNA (35-MER)	[3',4',5',5'',5]-100% 2D	0.5 ~ 1.0 mM
14	potassium chloride	natural abundance	60 mM
15	EDTA	natural abundance	10 uM

Chem. Shift Complete5

Sequence coverage: 65.7 %, Completeness: 27.1 %, Completeness (bb): 20.2 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	27.1 % (758 of 2795)	33.5 % (513 of 1530)	18.5 % (216 of 1165)	29.0 % (29 of 100)
Suger, PO4	20.2 % (388 of 1925)	28.1 % (295 of 1050)	10.6 % (93 of 875)
Nucleobase	42.5 % (370 of 870)	45.4 % (218 of 480)	42.4 % (123 of 290)	29.0 % (29 of 100)
Aromatic	43.3 % (338 of 780)	47.7 % (186 of 390)	42.4 % (123 of 290)	29.0 % (29 of 100)

1. RNA (35-MER)

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 5.2

#	Name	Isotope labeling	Concentration
1	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	60 mM
3	EDTA	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 5.2

#	Name	Isotope labeling	Concentration
4	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
5	potassium chloride	natural abundance	60 mM
6	EDTA	natural abundance	10 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 5.2

#	Name	Isotope labeling	Concentration
7	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
8	potassium chloride	natural abundance	60 mM
9	EDTA	natural abundance	10 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 5.2

#	Name	Isotope labeling	Concentration
10	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
11	potassium chloride	natural abundance	60 mM
12	EDTA	natural abundance	10 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 5.2

#	Name	Isotope labeling	Concentration
13	RNA (35-MER)	[3',4',5',5'',5]-100% 2D	0.5 ~ 1.0 mM
14	potassium chloride	natural abundance	60 mM
15	EDTA	natural abundance	10 uM

Chem. Shift Complete6

Sequence coverage: 62.9 %, Completeness: 23.8 %, Completeness (bb): 16.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	23.8 % (798 of 3354)	29.6 % (543 of 1836)	15.5 % (216 of 1398)	32.5 % (39 of 120)
Suger, PO4	16.8 % (388 of 2310)	23.4 % (295 of 1260)	8.9 % (93 of 1050)
Nucleobase	39.3 % (410 of 1044)	43.1 % (248 of 576)	35.3 % (123 of 348)	32.5 % (39 of 120)
Aromatic	38.7 % (362 of 936)	42.7 % (200 of 468)	35.3 % (123 of 348)	32.5 % (39 of 120)

1. RNA (35-MER)

GGAGCCGUAU GCGGUAGUUC CGCACGUACG GAUCU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
2	potassium chloride	natural abundance	60 mM
3	EDTA	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	RNA (35-MER)	natural abundance	0.5 ~ 1.0 mM
5	potassium chloride	natural abundance	60 mM
6	EDTA	natural abundance	10 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 6.7

#	Name	Isotope labeling	Concentration
7	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
8	potassium chloride	natural abundance	60 mM
9	EDTA	natural abundance	10 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 6.7

#	Name	Isotope labeling	Concentration
10	RNA (35-MER)	[100% 13C; 100% 15N]	0.5 ~ 1.0 mM
11	potassium chloride	natural abundance	60 mM
12	EDTA	natural abundance	10 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 6.7

#	Name	Isotope labeling	Concentration
13	RNA (35-MER)	[3',4',5',5'',5]-100% 2D	0.5 ~ 1.0 mM
14	potassium chloride	natural abundance	60 mM
15	EDTA	natural abundance	10 uM

Release date

2014-02-23

Citation

Acid-base equilibria near neutral pH in the catalytic triad and the bulge of domain 5 of a bacterial group II intron
Pechlaner, M., Donghi, D., Zelenay, V., Sigel, R.K. O.
Not known