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BMRB: 17520

2LAC

Unmodified_ASL_Tyr

Authors

Denmon, A.P., Wang, J., Nikonowicz, E.P.

Assembly

Unmodified ASL Tyr

Entity

1. Unmodified ASL Tyr (polymer, Thiol state: not present), 17 monomers, 5505.273 Da Detail

GGGGACUGUA AAUCCCC

Formula weight

5505.273 Da

Source organism

Bacillus subtilis

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.9 %, Completeness (bb): 84.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	80.9 % (233 of 288)	77.9 % (116 of 149)	87.7 % (100 of 114)	12.5 % (1 of 8)	94.1 % (16 of 17)
Suger, PO4	84.8 % (173 of 204)	77.5 % (79 of 102)	91.8 % (78 of 85)		94.1 % (16 of 17)
Nucleobase	71.4 % (60 of 84)	78.7 % (37 of 47)	75.9 % (22 of 29)	12.5 % (1 of 8)
Aromatic	70.3 % (52 of 74)	78.4 % (29 of 37)	75.9 % (22 of 29)	12.5 % (1 of 8)

1. Unmod tyrASL

GGGGACUGUA AAUCCCC

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

Release date

2011-08-01

Citation

Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr)
Denmon, A.P., Wang, J., Nikonowicz, E.P.
J. Mol. Biol. (2011), 412, 285-303, PubMed 21782828 , DOI 10.1016/j.jmb.2011.07.010 , Abstract

Related entities 1. Unmodified ASL Tyr, : 1 : 1 : 1 entities Detail

Experiments performed 8 experiments Detail

1 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

3 2D HCN

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

4 2D 1H-1H TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

5 2D 31P-1H

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

6 2D HCCH-RELAY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

7 2D HCCH-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

8 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Unmod_tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium chloride	natural abundance		10 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17520_2lac.nef
Input source #2: Coordindates	2lac.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-------
GGGGACUGUAAAUCCCC
|||||||||||||||||
GGGGACUGUAAAUCCCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	17	0	0	100.0

Content subtype: combined_17520_2lac.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	309		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	274 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	42 (1)	hbond	70.6 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	135 (135)	.	100.0 (chain: A, length: 17)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 136
- ¹³C chemical shifts: 116
- ¹⁵N chemical shifts: 41
- ³¹P chemical shifts: 16

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	HO2'	4.65
2	G	N7	233.31
2	G	N9	169.81
2	G	P	-3.72
3	G	HO2'	4.64
3	G	N7	233.96
3	G	N9	169.52
3	G	P	-3.56
4	G	HO2'	4.68
4	G	N7	234.4
4	G	N9	169.15
4	G	P	-3.54
5	A	H62	7.91
5	A	H61	6.71
5	A	HO2'	4.63
5	A	N1	222.75
5	A	N3	214.03
5	A	N6	82.19
5	A	N7	231.26
5	A	N9	170.4
5	A	P	-3.9
6	C	HO2'	4.1
6	C	C2	159.94
6	C	C4	167.96
6	C	N1	152.25
6	C	N4	96.88
6	C	P	-4.23
7	U	HO2'	4.21
7	U	C2	154.6
7	U	C4	167.96
7	U	N1	144.62
7	U	P	-3.95
8	G	HO2'	4.58
8	G	N7	237.34
8	G	P	-3.72
9	U	HO2'	4.08
9	U	C2	155.36
9	U	C4	168.23
9	U	N1	143.16
9	U	P	-3.68
10	A	H61	6.59
10	A	HO2'	4.67
10	A	N1	224.51
10	A	N3	217.4
10	A	N6	77.82
10	A	N7	231.55
10	A	N9	168.42
10	A	P	-3.84
11	A	H61	6.95
11	A	N1	222.68
11	A	N3	216.01
11	A	N6	80.05
11	A	N7	231.47
11	A	N9	168.34
11	A	P	-3.45
12	A	H61	6.76
12	A	HO2'	4.51
12	A	N1	219.6
12	A	N3	219.6
12	A	N6	80.15
12	A	N7	234.84
12	A	N9	175.6
12	A	P	-3.86
13	U	HO2'	4.28
13	U	C2	153.8
13	U	C4	168.48
13	U	N1	146.81
13	U	P	-3.79
14	C	HO2'	4.27
14	C	C2	159.66
14	C	C4	168.27
14	C	N1	151.81
14	C	N4	97.9
14	C	P	-4.22
15	C	HO2'	4.34
15	C	C2	159.96
15	C	C4	168.37
15	C	N1	151.25
15	C	N4	97.4
15	C	P	-4.4
16	C	HO2'	4.27
16	C	C2	159.86
16	C	C4	168.4
16	C	N1	151.14
16	C	N4	97.46
16	C	P	-4.31
17	C	HO2'	3.97
17	C	C2	160.78
17	C	C4	168.69
17	C	N1	152.33
17	C	N4	96.54
17	C	P	-4.12

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	116	77.9
¹³C chemical shifts	114	100	87.7
¹⁵N chemical shifts	8	1	12.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	79	77.5
¹³C chemical shifts	85	78	91.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	37	78.7
¹³C chemical shifts	29	22	75.9
¹⁵N chemical shifts	8	1	12.5

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	13	13	100.0
¹³C chemical shifts	13	12	92.3

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 274
- Weight of restraints: 1.0 (274)
- Potential type of restraints: square-well-parabolic (274)
- Range of distance target values: 2.4, 9.4 (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: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 70.6%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: square-well-parabolic (42)
  - Range of distance target values: 2.0, 9.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 135
- Total number of restraints per polymer type: 135
- Weight of restraints: 1.0 (135)
- Potential type of restraints: square-well-parabolic (135)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Anticodon, Tyrosyl-tRNA, unmodified