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BMRB: 18532

2LUN

RNA Aptamer for B. anthracis Ribosomal Protein S8

Authors

Nikonowicz, E.P., Wang, J.

Assembly

RNA Aptamer for B. anthracis Ribosomal Protein S8

Entity

1. RNA Aptamer for B. anthracis Ribosomal Protein S8 (polymer, Thiol state: not present), 28 monomers, 9049.343 × 9 Da Detail

GGGCAGUGAU GCUUCGGCAU AUCAGCCC

Total weight

81444.086 Da

Max. entity weight

9049.343 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.6 %, Completeness (bb): 91.2 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	88.6 % (397 of 448)	89.4 % (220 of 246)	90.9 % (170 of 187)	46.7 % (7 of 15)
Suger, PO4	91.2 % (281 of 308)	92.3 % (155 of 168)	90.0 % (126 of 140)
Nucleobase	82.9 % (116 of 140)	83.3 % (65 of 78)	93.6 % (44 of 47)	46.7 % (7 of 15)
Aromatic	85.5 % (106 of 124)	88.7 % (55 of 62)	93.6 % (44 of 47)	46.7 % (7 of 15)

1. RNA

GGGCAGUGAU GCUUCGGCAU AUCAGCCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	RNA	[U-98% 13C; U-98% 15N]	1.5 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	[U-2H]	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

Release date

2013-12-15

Citation

An RNA Aptamer Takes an Unexpected Twist to Bind r-Protein S8
Donarski, J., Wang, J., Nikonowicz, E.P.
Unknown

Related entities 1. RNA Aptamer for B. anthracis Ribosomal Protein S8, : 1 : 1 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

2 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

3 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	RNA	[U-98% 13C; U-98% 15N]	1.5 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	[U-2H]	10 %

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	RNA	[U-98% 13C; U-98% 15N]	1.5 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	[U-2H]	10 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

6 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

7 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

9 2D 1H-31P HetCor

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

10 2D 1H-15N HNC-TOCSY-CH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Concentration
1	RNA	[U-98% 13C; U-98% 15N]	1.5 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	[U-2H]	10 %

11 2D 1H-13C H(N)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	RNA	[U-98% 13C; U-98% 15N]	1.5 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	[U-2H]	10 %

12 2D 1H-13C CCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

13 2D 1H-13C HCNC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

14 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

15 2D 1H-15N HCN

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-98% 13C; U-98% 15N]		1.6 (±0.1) mM
5	D2O	[U-2H]		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18532_2lun.nef
Input source #2: Coordindates	2lun.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): A vs Auth_asym_ID (model): A

--------10--------20--------
GGGCAGUGAUGCUUCGGCAUAUCAGCCC
||||||||||||||||||||||||||||
GGGCAGUGAUGCUUCGGCAUAUCAGCCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	28	0	0	100.0

Content subtype: combined_18532_2lun.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	486		100.0 (chain: A, length: 28)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	63 (1)	noe	78.6 (chain: A, length: 28)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	298 (1)	noe	100.0 (chain: A, length: 28)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	224 (224)	.	100.0 (chain: A, length: 28)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%

--------10--------20--------
GGGCAGUGAUGCUUCGGCAUAUCAGCCC
||||||||||||||||||||||||||||
GGGCAGUGAUGCUUCGGCAUAUCAGCCC

Total number of assignments
- ¹H chemical shifts: 220
- ¹³C chemical shifts: 201
- ¹⁵N chemical shifts: 65

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	N9	169.52
3	G	N7	234.08
3	G	N9	168.78
4	C	C2	159.54
4	C	C4	169.19
4	C	N4	97.75
5	A	N1	229.26
5	A	N3	214.81
5	A	N6	82.33
5	A	N7	230.52
5	A	N9	169.75
6	G	N7	235.42
6	G	N9	168.34
7	U	C2	154.73
7	U	C4	167.31
7	U	N1	145.07
8	G	C2	154.36
8	G	N7	236.76
8	G	N9	166.93
9	A	N1	223.17
9	A	N3	214.46
9	A	N6	82.12
9	A	N7	230.75
9	A	N9	168.93
10	U	C2	153.3
10	U	C4	169.58
11	G	N7	234.83
11	G	N9	169.82
12	C	C2	159.42
12	C	C4	169.24
12	C	N1	151.61
12	C	N4	99.29
13	U	C2	153.78
13	U	C4	168.48
14	U	C2	155.84
14	U	C4	169.55
14	U	N1	144.02
15	C	C2	160.81
15	C	C4	168.74
15	C	N1	150.77
15	C	N4	93.63
16	G	C2	156.38
16	G	C6	162.35
16	G	N7	231.71
16	G	N9	171.75
17	G	N7	233.12
17	G	N9	170.41
18	C	C2	159.56
18	C	C4	169.27
18	C	N1	152.02
18	C	N4	97.49
19	A	N1	222.2
19	A	N3	213.82
19	A	N6	83.56
19	A	N7	231.19
19	A	N9	170.93
20	U	C2	153.7
20	U	C4	168.97
20	U	N1	146.55
21	A	N1	225.47
21	A	N3	215.74
21	A	N6	80.84
21	A	N7	231.41
21	A	N9	169.23
22	U	C2	152.98
22	U	C4	168.67
22	U	N1	146.35
23	C	C2	159.74
23	C	C4	168.94
23	C	N1	151.68
23	C	N4	98.16
24	A	N1	229.7
24	A	N3	213.9
24	A	N6	81.7
24	A	N7	231.04
24	A	N9	169.08
25	G	N7	233.56
25	G	N9	168.34
26	C	C2	159.6
26	C	C4	168.93
26	C	N1	152.1
26	C	N4	98.62
27	C	C2	155.72
27	C	C4	169.32
27	C	N4	98.31
28	C	C2	160.66
28	C	C4	169.52
28	C	N1	153.64
28	C	N4	97.18

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	246	220	89.4
¹³C chemical shifts	187	170	90.9
¹⁵N chemical shifts	15	7	46.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	155	92.3
¹³C chemical shifts	140	126	90.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	65	83.3
¹³C chemical shifts	47	44	93.6
¹⁵N chemical shifts	15	7	46.7

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0
¹³C chemical shifts	19	18	94.7

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 78.6%
- Total number of restraints: 63
- Weight of restraints: 1.0 (63)
- Potential type of restraints: square-well-parabolic (63)
- Range of distance target values: 1.75, 3.6 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
  - Total number of restraints: 298
  - Weight of restraints: 1.0 (298)
  - Potential type of restraints: square-well-parabolic (298)
  - Range of distance target values: 2.4, 4.4 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of restraints: 224
- Total number of restraints per polymer type: 224
- Weight of restraints: 1.0 (224)
- Potential type of restraints: square-well-parabolic (224)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Aptamer, Non-canonical base pairs, Protein S8, Ribosome, Selex

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Found 1 Document (0.352 seconds)

BMRB: 18532

Sample #1

Sample #2

Related entities 1. RNA Aptamer for B. anthracis Ribosomal Protein S8, : 1 : 1 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail