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BMRB: 17572

2LBQ

i6A37_tyrASL

Authors

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

Assembly

i6A37 tyrASL

Entity

1. i6A37 tyrASL (polymer, Thiol state: not present), 17 monomers, 5575.406 Da Detail

GGGGACUGUA XAUCCCC

Formula weight

5575.406 Da

Source organism

Bacillus subtilis

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 80.1 %, Completeness (bb): 82.4 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	80.1 % (205 of 256)	78.7 % (111 of 141)	87.9 % (94 of 107)	0.0 % (0 of 8)
Suger, PO4	82.4 % (145 of 176)	77.1 % (74 of 96)	88.7 % (71 of 80)
Nucleobase	75.0 % (60 of 80)	82.2 % (37 of 45)	85.2 % (23 of 27)	0.0 % (0 of 8)
Aromatic	71.4 % (50 of 70)	77.1 % (27 of 35)	85.2 % (23 of 27)	0.0 % (0 of 8)

1. i6A37 tyrASL

GGGGACUGUA XAUCCCC

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	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

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 17517 released on 2011-08-01
    Title Pseudouridine_ASL_Tyr
  BMRB: 17520 released on 2011-08-01
    Title Unmodified_ASL_Tyr
  BMRB: 17573 released on 2011-08-01
    Title Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR

Related entities 1. i6A37 tyrASL, : 1 : 2 : 1 entities Detail

Experiments performed 7 experiments Detail

1 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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

3 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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

4 2D 1H-13C Long Range 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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

5 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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

7 2D HCNC

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	i6A tyrASL	[U-100% 13C; U-100% 15N]		2.0 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		10 mM
4	EDTA	natural abundance		0.02 mM
5	D2O	natural abundance		100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17572_2lbq.nef
Input source #2: Coordindates	2lbq.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:10:A:O3'	1:11:6IA:P	unknown	unknown	n/a
1:11:6IA:O3'	1:12:A:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	11	6IA	N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10-------
GGGGACUGUAXAUCCCC
|||||||||||||||||
GGGGACUGUAXAUCCCC

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_17572_2lbq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	266		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	278 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3 (1)	hbond	11.8 (chain: A, length: 17)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	28 (1)	hbond	58.8 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	122 (122)	.	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: 141
- ¹³C chemical shifts: 101
- ¹⁵N chemical shifts: 24

Completeness of assignments

Entity_assemble_ID: A

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
11	6IA

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	HO2'	4.6
2	G	N7	232.12
3	G	HO2'	4.59
3	G	N7	235.2
4	G	HO2'	4.5
4	G	N7	234.93
5	A	H62	6.66
5	A	HO2'	4.53
5	A	N1	223.1
5	A	N3	212.74
5	A	N6	80.24
5	A	N7	230.03
6	C	HO2'	4.01
6	C	N4	96.12
7	U	HO2'	4.22
8	G	HO2'	4.71
8	G	N7	235.49
9	U	HO2'	4.22
10	A	H62	6.39
10	A	HO2'	4.82
10	A	N1	224.51
10	A	N3	215.43
10	A	N6	78.96
10	A	N7	231.56
12	A	H62	6.46
12	A	HO2'	4.5
12	A	N3	214.59
12	A	N6	79.98
12	A	N7	229.83
13	U	HO2'	4.23
14	C	HO2'	4.25
14	C	N4	97.98
15	C	HO2'	4.32
15	C	N4	97.46
16	C	HO2'	4.23
16	C	N4	97.6
17	C	HO2'	3.96
17	C	N4	96.57

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	141	111	78.7
¹³C chemical shifts	107	94	87.9
¹⁵N chemical shifts	8	0	0.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	74	77.1
¹³C chemical shifts	80	71	88.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	37	82.2
¹³C chemical shifts	27	23	85.2
¹⁵N chemical shifts	8	0	0.0

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	11	11	100.0
¹³C chemical shifts	11	9	81.8

Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

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: 278
- Weight of restraints: 1.0 (278)
- Potential type of restraints: square-well-parabolic (278)
- Range of distance target values: 2.4, 4.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 11.8%
  - Total number of restraints: 3
  - Weight of restraints: 1.0 (3)
  - Potential type of restraints: square-well-parabolic (3)
  - Range of distance target values: 4.25, 4.25 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 58.8%
    - Total number of restraints: 28
    - Weight of restraints: 1.0 (28)
    - Potential type of restraints: square-well-parabolic (28)
    - Range of distance target values: 2.1, 3.05 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 122
- Total number of restraints per polymer type: 122
- Weight of restraints: 1.0 (122)
- Potential type of restraints: square-well-parabolic (122)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Anticodon stem loop, i6A, Tyrosyl-tRNA