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BMRB: 17563

2LBJ

Glycyl-tRNA(GCC) anticodon stem-loop from Bacillus subtilis

Authors

Chang, A.T., Nikonowicz, E.P.

Assembly

glycyl-tRNA anticodon stem-loops

Entity

1. glycyl-tRNA anticodon stem-loops (polymer, Thiol state: not present), 17 monomers, 5497.249 Da Detail

GGGCCUUGCC AAGGUCC

Formula weight

5497.249 Da

Source organism

Bacillus subtilis

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 75.0 %, Completeness (bb): 77.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	75.0 % (198 of 264)	71.5 % (108 of 151)	79.6 % (90 of 113)
Suger, PO4	77.0 % (144 of 187)	79.4 % (81 of 102)	74.1 % (63 of 85)
Nucleobase	70.1 % (54 of 77)	55.1 % (27 of 49)	96.4 % (27 of 28)
Aromatic	83.1 % (54 of 65)	73.0 % (27 of 37)	96.4 % (27 of 28)

1. glycyl-tRNA

GGGCCUUGCC AAGGUCC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA	[U-98% 13C; U-98% 15N]		0.02 ~ 0.04 mM
2	D2O	natural abundance		100 %
3	KH2PO4	natural abundance		10 mM
4	K2HPO4	natural abundance		10 mM
5	KCl	natural abundance		10 mM
6	EDTA	natural abundance		0.2 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	RNA	natural abundance		0.02 ~ 0.04 mM
8	D2O	natural abundance		100 %
9	KH2PO4	natural abundance		10 mM
10	K2HPO4	natural abundance		10 mM
11	KCl	natural abundance		10 mM
12	EDTA	natural abundance		0.2 mM

Release date

2012-04-03

Citation

Structure solution of three glycyl-tRNA anticodon stem-loops
Chang, A.T., Nikonowicz, E.P.
Not known

Related entities 1. glycyl-tRNA anticodon stem-loops, : 1 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA	[U-98% 13C; U-98% 15N]		0.02 ~ 0.04 mM
2	D2O	natural abundance		100 %
3	KH2PO4	natural abundance		10 mM
4	K2HPO4	natural abundance		10 mM
5	KCl	natural abundance		10 mM
6	EDTA	natural abundance		0.2 mM

2 2D 1H-1H COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA	[U-98% 13C; U-98% 15N]		0.02 ~ 0.04 mM
2	D2O	natural abundance		100 %
3	KH2PO4	natural abundance		10 mM
4	K2HPO4	natural abundance		10 mM
5	KCl	natural abundance		10 mM
6	EDTA	natural abundance		0.2 mM

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	RNA	natural abundance		0.02 ~ 0.04 mM
8	D2O	natural abundance		100 %
9	KH2PO4	natural abundance		10 mM
10	K2HPO4	natural abundance		10 mM
11	KCl	natural abundance		10 mM
12	EDTA	natural abundance		0.2 mM

4 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA	[U-98% 13C; U-98% 15N]		0.02 ~ 0.04 mM
2	D2O	natural abundance		100 %
3	KH2PO4	natural abundance		10 mM
4	K2HPO4	natural abundance		10 mM
5	KCl	natural abundance		10 mM
6	EDTA	natural abundance		0.2 mM

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA	[U-98% 13C; U-98% 15N]		0.02 ~ 0.04 mM
2	D2O	natural abundance		100 %
3	KH2PO4	natural abundance		10 mM
4	K2HPO4	natural abundance		10 mM
5	KCl	natural abundance		10 mM
6	EDTA	natural abundance		0.2 mM

6 2D HCN

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA	[U-98% 13C; U-98% 15N]		0.02 ~ 0.04 mM
2	D2O	natural abundance		100 %
3	KH2PO4	natural abundance		10 mM
4	K2HPO4	natural abundance		10 mM
5	KCl	natural abundance		10 mM
6	EDTA	natural abundance		0.2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17563_2lbj.nef
Input source #2: Coordindates	2lbj.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-------
GGGCCUUGCCAAGGUCC
|||||||||||||||||
GGGCCUUGCCAAGGUCC

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_17563_2lbj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	198		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	211 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	28 (1)	hbond	58.8 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	131 (131)	.	100.0 (chain: A, length: 17)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 108
  - ¹³C chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 211
- Weight of restraints: 1.0 (211)
- Potential type of restraints: square-well-parabolic (211)
- Range of distance target values: 1.2, 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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - 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: 131
- Total number of restraints per polymer type: 131
- Weight of restraints: 1.0 (131)
- Potential type of restraints: square-well-parabolic (131)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords anticodon stem-loop, NMR, tRNA