BMRBj - BMREntryMaster

Found 1 Document (0.583 seconds)

BMRB: 18881

2M1V

NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid

Authors

Skilandat, M., Sigel, R.K. O.

Assembly

d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid

Entity

1. RNA (29-MER) (polymer, Thiol state: not present), 29 monomers, 9364.517 Da Detail

GGAGUAUGUA UUGGCACUGA GCAUACUCC

2. DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3') (polymer, Thiol state: not present), 7 monomers, 2176.382 Da Detail

CAGTGTC

Total weight

11540.898 Da

Max. entity weight

9364.517 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 63.0 %, Completeness (bb): 51.1 % Detail

Polymer type: polyribonucleotide polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	63.0 % (335 of 532)	82.6 % (265 of 321)	28.7 % (56 of 195)	87.5 % (14 of 16)
Suger, PO4	51.1 % (188 of 368)	75.8 % (169 of 223)	13.1 % (19 of 145)
Nucleobase	89.6 % (147 of 164)	98.0 % (96 of 98)	74.0 % (37 of 50)	87.5 % (14 of 16)
Aromatic	88.4 % (129 of 146)	97.5 % (78 of 80)	74.0 % (37 of 50)	87.5 % (14 of 16)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. RNA (29-MER)

GGAGUAUGUA UUGGCACUGA GCAUACUCC

2. DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3')

CAGTGTC

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
2	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
3	potassium chloride	natural abundance	110 mM
4	EDTA	natural abundance	10 uM
5	D2O	natural abundance	100 %

Sample #2

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

#	Name	Isotope labeling	Concentration
6	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
7	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
8	potassium chloride	natural abundance	110 mM
9	EDTA	natural abundance	10 uM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

Sample #3

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

#	Name	Isotope labeling	Concentration
12	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
13	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
14	potassium chloride	natural abundance	110 mM
15	EDTA	natural abundance	10 uM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

Sample #4

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

#	Name	Isotope labeling	Concentration
18	RNA_(29-MER)	natural abundance	0.5 ~ 1.0 mM
19	potassium chloride	natural abundance	10 mM
20	EDTA	natural abundance	10 uM
21	D2O	natural abundance	100 %

Sample #5

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

#	Name	Isotope labeling	Concentration
22	RNA_(29-MER)	[3',4',5',5'',5]-100% 2H	0.6 ~ 0.9 mM
23	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7-1.0 mM
24	potassium chloride	natural abundance	110 mM
25	EDTA	natural abundance	10 uM

Sample #6

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

#	Name	Isotope labeling	Concentration
26	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
27	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
28	potassium chloride	natural abundance	110 mM
29	EDTA	natural abundance	10 uM
30	D2O	natural abundance	100 %

Sample #7

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

#	Name	Isotope labeling	Concentration
31	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
32	potassium chloride	natural abundance	10 mM
33	EDTA	natural abundance	10 uM
34	H2O	natural abundance	90 %
35	D2O	natural abundance	10 %

Sample #8

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

#	Name	Isotope labeling	Concentration
36	RNA (29-MER)	natural abundance	0.5 ~ 1.0 mM
37	potassium chloride	natural abundance	10 mM
38	EDTA	natural abundance	10 uM
39	H2O	natural abundance	90 %
40	D2O	natural abundance	10 %

Release date

2014-06-08

Citation

Determinants of DNA cleavage site recognition in group II intron retrohoming - Solution structure and metal-ion binding sites of the Sc.ai5gamma RNA:DNA contact
Skilandat, M., Sigel, R.K. O.
Not known

Related entities 1. RNA (29-MER), : 1 : 2 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
1	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
2	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
3	potassium chloride	natural abundance	110 mM
4	EDTA	natural abundance	10 uM
5	D2O	natural abundance	100 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
1	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
2	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
3	potassium chloride	natural abundance	110 mM
4	EDTA	natural abundance	10 uM
5	D2O	natural abundance	100 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
1	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
2	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
3	potassium chloride	natural abundance	110 mM
4	EDTA	natural abundance	10 uM
5	D2O	natural abundance	100 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
22	RNA_(29-MER)	[3',4',5',5'',5]-100% 2H	0.6 ~ 0.9 mM
23	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7-1.0 mM
24	potassium chloride	natural abundance	110 mM
25	EDTA	natural abundance	10 uM

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
18	RNA_(29-MER)	natural abundance	0.5 ~ 1.0 mM
19	potassium chloride	natural abundance	10 mM
20	EDTA	natural abundance	10 uM
21	D2O	natural abundance	100 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
18	RNA_(29-MER)	natural abundance	0.5 ~ 1.0 mM
19	potassium chloride	natural abundance	10 mM
20	EDTA	natural abundance	10 uM
21	D2O	natural abundance	100 %

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
12	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
13	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
14	potassium chloride	natural abundance	110 mM
15	EDTA	natural abundance	10 uM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
7	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
8	potassium chloride	natural abundance	110 mM
9	EDTA	natural abundance	10 uM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
26	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
27	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
28	potassium chloride	natural abundance	110 mM
29	EDTA	natural abundance	10 uM
30	D2O	natural abundance	100 %

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
26	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
27	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
28	potassium chloride	natural abundance	110 mM
29	EDTA	natural abundance	10 uM
30	D2O	natural abundance	100 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
7	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
8	potassium chloride	natural abundance	110 mM
9	EDTA	natural abundance	10 uM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

12 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
7	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
8	potassium chloride	natural abundance	110 mM
9	EDTA	natural abundance	10 uM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

13 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
7	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
8	potassium chloride	natural abundance	110 mM
9	EDTA	natural abundance	10 uM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

14 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
26	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
27	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
28	potassium chloride	natural abundance	110 mM
29	EDTA	natural abundance	10 uM
30	D2O	natural abundance	100 %

15 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
26	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
27	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
28	potassium chloride	natural abundance	110 mM
29	EDTA	natural abundance	10 uM
30	D2O	natural abundance	100 %

16 1D 31P

Instrument

Bruker Avance - 500 MHz CRYO 5 mm QNP with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Concentration
1	RNA_(29-MER)	natural abundance	0.6 ~ 0.9 mM
2	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
3	potassium chloride	natural abundance	110 mM
4	EDTA	natural abundance	10 uM
5	D2O	natural abundance	100 %

17 F1, F2 X-filtered 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
12	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
13	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
14	potassium chloride	natural abundance	110 mM
15	EDTA	natural abundance	10 uM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

18 F1, F2 X-filtered 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance with actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
12	RNA_(29-MER)	[U-100% 13C; U-100% 15N]	0.6 ~ 0.9 mM
13	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	natural abundance	0.7 ~ 1.0 mM
14	potassium chloride	natural abundance	110 mM
15	EDTA	natural abundance	10 uM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

nullKeywords DNA, group II intron, hybrid, retrohoming, reverse splicing, ribozyme, RNA

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Found 1 Document (0.583 seconds)

BMRB: 18881

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Related entities 1. RNA (29-MER), : 1 : 2 entities Detail

Experiments performed 18 experiments Detail

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