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BMRB: 18974

2MER

Modified Helix 69

Authors

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

Assembly

HELIX 69

Entity

1. HELIX 69 (polymer, Thiol state: not present), 19 monomers, 6140.644 Da Detail

GGCCGXAACX AXAACGGUC

Formula weight

6140.644 Da

Source organism

Escherichia coli

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 84.2 %, Completeness: 71.5 %, Completeness (bb): 63.1 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	71.5 % (176 of 246)	95.7 % (133 of 139)	40.2 % (43 of 107)
Suger, PO4	63.1 % (111 of 176)	99.0 % (95 of 96)	20.0 % (16 of 80)
Nucleobase	92.9 % (65 of 70)	88.4 % (38 of 43)	100.0 % (27 of 27)
Aromatic	98.3 % (59 of 60)	97.0 % (32 of 33)	100.0 % (27 of 27)

1. HELIX 69

GGCCGXAACX AXAACGGUC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	natural abundance		100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
6	HELIX_69	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	D2O	natural abundance		10 %
11	H2O	natural abundance		90 %

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

Related entities 1. HELIX 69, : 1 : 14 : 2 entities Detail

Experiments performed 7 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 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	natural abundance		100 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	natural abundance		100 %

3 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	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 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	natural abundance		100 %

5 2D 1H-31P HETCOR

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	natural abundance		100 %

6 1D 31P

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	HELIX_69	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	D2O	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 283.2 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
6	HELIX_69	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	D2O	natural abundance		10 %
11	H2O	natural abundance		90 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18974_2mer.nef
Input source #2: Coordindates	2mer.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)
1:5:G:O3'	1:6:PSU:P	unknown	unknown	n/a
1:6:PSU:O3'	1:7:A:P	unknown	unknown	n/a
1:9:C:O3'	1:10:PSU:P	unknown	unknown	n/a
1:10:PSU:O3'	1:11:A:P	unknown	unknown	n/a
1:11:A:O3'	1:12:PSU:P	unknown	unknown	n/a
1:12:PSU:O3'	1:13:A:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	10	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	12	PSU	PSEUDOURIDINE-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---------
GGCCGXAACXAXAACGGUC
|||||||||||||||||||
GGCCGXAACXAXAACGGUC

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_18974_2mer.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	201		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_5	OK	27 (1)	undefined	63.2 (chain: A, length: 19)
4	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	224 (1)	noe	100.0 (chain: A, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	127 (127)	.	100.0 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 155
  - ¹³C chemical shifts: 46
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

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: 2.25, 4.5 (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: 63.2%
    - Total number of restraints: 27
    - Weight of restraints: 1.0 (27)
    - Potential type of restraints: square-well-parabolic (27)
    - 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
    - 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%
        --------10--------- GGCCGXAACXAXAACGGUC ||||||||||||||||||| GGCCGXAACXAXAACGGUC
      - Total number of restraints: 224
        Intra-residue restraints, i = j : 81
        Sequential restraints, | i - j | = 1 : 133
        Backbone-backbone: 27
        Backbone-side chain: 80
        Side chain-side chain: 26
        Medium range restraints, 1 < | i - j | < 5 : 5
        Backbone-backbone: 1
        Backbone-side chain: 3
        Side chain-side chain: 1
        Long range restraints, | i - j | >= 5 : 5
      - Weight of restraints: 1.0 (224)
        Intra-residue restraints, i = j : 1.0 (81)
        Sequential restraints, | i - j | = 1 : 1.0 (133)
        Backbone-backbone: 1.0 (27)
        Backbone-side chain: 1.0 (80)
        Side chain-side chain: 1.0 (26)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (5)
        Backbone-backbone: 1.0 (1)
        Backbone-side chain: 1.0 (3)
        Side chain-side chain: 1.0 (1)
        Long range restraints, | i - j | >= 5 : 1.0 (5)
      - Potential type of restraints: square-well-parabolic (224)
        Intra-residue restraints, i = j : square-well-parabolic (81)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (133)
        Backbone-backbone: square-well-parabolic (27)
        Backbone-side chain: square-well-parabolic (80)
        Side chain-side chain: square-well-parabolic (26)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (5)
        Backbone-backbone: square-well-parabolic (1)
        Backbone-side chain: square-well-parabolic (3)
        Side chain-side chain: square-well-parabolic (1)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (5)
      - Range of distance target values: 2.2, 5.0 (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: 127
- Total number of restraints per polymer type: 127
- Weight of restraints: 1.0 (127)
- Potential type of restraints: square-well-parabolic (127)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Helix 69, Pseudouridine, Ribosomal, RNA