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BMRB: 25291

2MVY

RNA duplex

Authors

Lynch, S.R., Kool, E.T.

Assembly

RNA duplex

Entity

1. RNA duplex (polymer, Thiol state: not present), 10 monomers, 3239.920 × 2 Da Detail

GGACUAGUCC

Total weight

6479.84 Da

Max. entity weight

3239.92 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 78.8 %, Completeness (bb): 72.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	78.8 % (130 of 165)	84.1 % (74 of 88)	71.6 % (48 of 67)	80.0 % (8 of 10)
Suger, PO4	72.5 % (87 of 120)	80.0 % (48 of 60)	62.0 % (31 of 50)	80.0 % (8 of 10)
Nucleobase	95.6 % (43 of 45)	92.9 % (26 of 28)	100.0 % (17 of 17)
Aromatic	97.4 % (38 of 39)	95.5 % (21 of 22)	100.0 % (17 of 17)

1. RNA

GGACUAGUCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	0.2 mM
2	sodium chloride	natural abundance	100 mM
3	EDTA	natural abundance	0.1 mM
4	sodium phosphate	natural abundance	10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

Release date

2015-09-27

Citation

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification
Roost, C., Lynch, S.R., Batista, P.J., Qu, K., Chang, H.Y., Kool, E.T.
J. Am. Chem. Soc. (2015), 137, 2107-2115, PubMed 25611135 , DOI 10.1021/ja513080v , Abstract

Experiments performed 7 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

2 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

4 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	0.2 mM
2	sodium chloride	natural abundance	100 mM
3	EDTA	natural abundance	0.1 mM
4	sodium phosphate	natural abundance	10 mM

7 2D 1H-31P COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25291_2mvy.nef
Input source #2: Coordindates	2mvy.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): 1 vs Auth_asym_ID (model): 1
Entity_assembly_ID (NMR): 2 vs Auth_asym_ID (model): 2

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
1	1	10	0	0	100.0
2	2	10	0	0	100.0

Content subtype: combined_25291_2mvy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	133		100.0 (chain: 1, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	382 (1)	noe	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	172 (172)	.	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 77
  - ¹³C chemical shifts: 48
  - ³¹P chemical shifts: 8
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	P	0.079
3	A	H61	8.414
3	A	H62	6.968
3	A	P	-0.116
4	C	P	-0.276
5	U	P	-0.437
6	A	H61	7.706
6	A	P	0.023
8	U	P	-0.758
9	C	P	-0.258
10	C	P	-0.223

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	74	84.1
¹³C chemical shifts	67	48	71.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	48	80.0
¹³C chemical shifts	50	31	62.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	26	92.9
¹³C chemical shifts	17	17	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	7	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 382
- Weight of restraints: 1.0 (382)
- Potential type of restraints: square-well-parabolic (382)
- Range of distance target values: 1.7, 4.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 172
- Total number of restraints per polymer type: 172
- Weight of restraints: 1.0 (172)
- Potential type of restraints: square-well-parabolic (172)
- Dihedral angle restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2

Keywords RNA duplex

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Found 1 Document (0.348 seconds)

BMRB: 25291

Sample #1

Sample #2

Experiments performed 7 experiments Detail

Instrument

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NMR combined restraints 4 contents Detail