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Found 1 Document (0.486 seconds)

BMRB: 18975

2MEQ

Unmodified Helix 69

Authors

JIANG, J., ADURI, R., CHOW, C.S., SANTALUCIA, J.

Assembly

Unmodified Helix 69

Entity

1. Unmodified Helix 69 (polymer), 19 monomers, 6140.644 Da Detail

GGCCGUAACU AUAACGGUC

Formula weight

6140.644 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	98.0 % (288 of 294)	96.4 % (160 of 166)	100.0 % (128 of 128)
Suger, PO4	100.0 % (209 of 209)	100.0 % (114 of 114)	100.0 % (95 of 95)
Nucleobase	92.9 % (79 of 85)	88.5 % (46 of 52)	100.0 % (33 of 33)
Aromatic	94.7 % (71 of 75)	90.5 % (38 of 42)	100.0 % (33 of 33)

1. RNA

GGCCGUAACU AUAACGGUC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
6	RNA	natural abundance	1.0 mM
7	Potassium Phosphate	natural abundance	10 mM
8	Potassium Chloride	natural abundance	50 mM
9	EDTA	natural abundance	0.1 mM
10	D20	natural abundance	90 %
11	H2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
12	RNA	[U-100% 13C; U-100% 15N]	1.0 mM
13	Potassium Phosphate	natural abundance	10 mM
14	Potassium Chloride	natural abundance	50 mM
15	EDTA	natural abundance	0.1 mM
16	D20	natural abundance	100 %

Release date

2014-01-01

Citation

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations
Jiang, J., Aduri, R., Chow, C.S., Santalucia, J.
Nucleic Acids Res. (2014), 42, 3971-3981, PubMed 24371282 , DOI 10.1093/nar/gkt1329 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18974 released on 2014-01-01
Title Modified Helix 69

Related entities 1. Unmodified Helix 69, : 109 : 2 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-13C NATURAL ABUNDANCE HMQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

3 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

4 3D 1H-1H-1H TOCSY-NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

5 2D 1H-31P HETCOR

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

6 1D 31P

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	1.0 mM
2	Potassium Phosphate	natural abundance	10 mM
3	Potassium Chloride	natural abundance	50 mM
4	EDTA	natural abundance	0.1 mM
5	D20	natural abundance	100 %

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
6	RNA	natural abundance	1.0 mM
7	Potassium Phosphate	natural abundance	10 mM
8	Potassium Chloride	natural abundance	50 mM
9	EDTA	natural abundance	0.1 mM
10	D20	natural abundance	90 %
11	H2O	natural abundance	10 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
12	RNA	[U-100% 13C; U-100% 15N]	1.0 mM
13	Potassium Phosphate	natural abundance	10 mM
14	Potassium Chloride	natural abundance	50 mM
15	EDTA	natural abundance	0.1 mM
16	D20	natural abundance	100 %

9 3D 1H-13C-1H HCCH-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
12	RNA	[U-100% 13C; U-100% 15N]	1.0 mM
13	Potassium Phosphate	natural abundance	10 mM
14	Potassium Chloride	natural abundance	50 mM
15	EDTA	natural abundance	0.1 mM
16	D20	natural abundance	100 %

10 3D 1H-13C-1H HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
12	RNA	[U-100% 13C; U-100% 15N]	1.0 mM
13	Potassium Phosphate	natural abundance	10 mM
14	Potassium Chloride	natural abundance	50 mM
15	EDTA	natural abundance	0.1 mM
16	D20	natural abundance	100 %

11 3D 1H-13C-13C HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
12	RNA	[U-100% 13C; U-100% 15N]	1.0 mM
13	Potassium Phosphate	natural abundance	10 mM
14	Potassium Chloride	natural abundance	50 mM
15	EDTA	natural abundance	0.1 mM
16	D20	natural abundance	100 %

12 3D 1H-1H-13C NOESY-HMQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.3

#	Name	Isotope labeling	Concentration
12	RNA	[U-100% 13C; U-100% 15N]	1.0 mM
13	Potassium Phosphate	natural abundance	10 mM
14	Potassium Chloride	natural abundance	50 mM
15	EDTA	natural abundance	0.1 mM
16	D20	natural abundance	100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18975_2meq.nef
Input source #2: Coordindates	2meq.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---------
GGCCGUAACUAUAACGGUC
|||||||||||||||||||
GGCCGUAACUAUAACGGUC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	19	0	0	100.0

Content subtype: combined_18975_2meq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	288		100.0 (chain: A, length: 19)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	22 (1)	undefined	52.6 (chain: A, length: 19)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	13 (1)	noe	52.6 (chain: A, length: 19)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	241 (1)	noe	100.0 (chain: A, length: 19)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	24 (1)	undefined	52.6 (chain: A, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	129 (129)	.	100.0 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 160
  - ¹³C chemical shifts: 128
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	166	160	96.4
¹³C chemical shifts	128	128	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	114	100.0
¹³C chemical shifts	95	95	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	46	88.5
¹³C chemical shifts	33	33	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	15	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 52.6%
- Total number of restraints: 22
- Weight of restraints: 1.0 (22)
- Potential type of restraints: square-well-parabolic (22)
- Range of distance target values: 3.2, 6.5 (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: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 52.6%
  - Total number of restraints: 13
  - Weight of restraints: 1.0 (13)
  - Potential type of restraints: square-well-parabolic (13)
  - Range of distance target values: 2.1, 6.8 (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_6
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
    - Total number of restraints: 241
    - Weight of restraints: 1.0 (241)
    - Potential type of restraints: square-well-parabolic (241)
    - Range of distance target values: 2.3, 5.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: OK
      - Experiment type: undefined
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 52.6%
        --------10--------- GGCCGUAACUAUAACGGUC ||||| ||||| GGCCG.........CGGUC
      - Total number of restraints: 24
        Long range restraints, | i - j | >= 5 : 10
        Total hydrogen bond restraints: 14
      - Weight of restraints: 1.0 (24)
        Long range restraints, | i - j | >= 5 : 1.0 (10)
        Total hydrogen bond restraints: 1.0 (14)
      - Potential type of restraints: square-well-parabolic (24)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (10)
        Total hydrogen bond restraints: square-well-parabolic (14)
      - Range of distance target values: 2.7, 10.7 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 129
- Total number of restraints per polymer type: 129
- Weight of restraints: 1.0 (129)
- Potential type of restraints: square-well-parabolic (129)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Helix 69, Ribosomal, RNA

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Found 1 Document (0.486 seconds)

BMRB: 18975

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Unmodified Helix 69, : 109 : 2 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 7 contents Detail