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Found 1 Document (0.395 seconds)

BMRB: 25164

2MTK

NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

Authors

Bonneau, E., Legault, P.

Assembly

three-way junction from the VS ribozyme

Entity

1. RNA (47-MER) (polymer, Thiol state: not present), 47 monomers, 15180.93 Da Detail

GGACCUCCCG UCCUUGGACG GUCGAGCGAA AGCUUGUGAU UGGUCCG

2. MAGNESIUM ION (non-polymer), 24.305 × 6 Da
3. WATER (water), 18.015 × 10 Da

Total weight

15326.76 Da

Max. entity weight

15180.93 Da

Source organism

Neurospora crassa

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.4 %, Completeness (bb): 86.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	89.4 % (673 of 753)	87.9 % (363 of 413)	91.4 % (286 of 313)	88.9 % (24 of 27)
Suger, PO4	86.5 % (447 of 517)	84.8 % (239 of 282)	88.5 % (208 of 235)
Nucleobase	95.8 % (226 of 236)	94.7 % (124 of 131)	100.0 % (78 of 78)	88.9 % (24 of 27)
Aromatic	97.1 % (204 of 210)	97.1 % (102 of 105)	100.0 % (78 of 78)	88.9 % (24 of 27)

1. RNA (47-MER)

GGACCUCCCG UCCUUGGACG GUCGAGCGAA AGCUUGUGAU UGGUCCG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
10	J345-3	[U-100% 13C; U-100% 15N]	2.0 mM
11	KCl	natural abundance	50 mM
12	MgCl2	natural abundance	5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Release date

2014-10-13

Citation

Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
Bonneau, E., Legault, P.
Biochemistry (2014), 53, 6264-6275, PubMed 25238589 , DOI 10.1021/bi500826n , Abstract

Related entities 1. RNA (47-MER), : 1 : 1 entities Detail

Experiments performed 14 experiments Detail

1 1D flip-back watergate 1H

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-15N HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 2D 1H-15N HSQC NH2 only

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 2D 1H-13C HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

6 3D 13C-edited HMQC-NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

7 3D CT-HCCH-COSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

8 3D HCCH-TOCSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

9 3D 15N-edited NOESY-HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
10	J345-3	[U-100% 13C; U-100% 15N]	2.0 mM
11	KCl	natural abundance	50 mM
12	MgCl2	natural abundance	5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

10 2D H(NC)-TOCSY-(C)H for guanosine residues

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
10	J345-3	[U-100% 13C; U-100% 15N]	2.0 mM
11	KCl	natural abundance	50 mM
12	MgCl2	natural abundance	5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

11 2D 1H-13C HMQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

12 2D 1H-15N MQ-(HC)N(C)H

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	J345-2	[U-100% 13C; U-100% 15N]	2.0 mM
7	KCl	natural abundance	50 mM
8	MgCl2	natural abundance	5 mM
9	D2O	natural abundance	100 %

13 2D 1H-15N CPMG-NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

14 2D HNN-COSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	J345-1	[U-100% 15N]	1.5 ~ 2.0 mM
2	KCl	natural abundance	50 mM
3	MgCl2	natural abundance	5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25164_2mtk.nef
Input source #2: Coordindates	2mtk.cif
Diamagnetism of the molecular assembly	False (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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Distance (Å)
F:null:MG:MG	H:null:HOH:O	1.837
G:null:MG:MG	H:null:HOH:O	1.838
F:null:MG:MG	H:null:HOH:O	1.838
E:null:MG:MG	H:null:HOH:O	1.839
B:null:MG:MG	H:null:HOH:O	1.839
E:null:MG:MG	H:null:HOH:O	1.839
E:null:MG:MG	H:null:HOH:O	1.839
D:null:MG:MG	H:null:HOH:O	1.839
F:null:MG:MG	H:null:HOH:O	1.839
C:null:MG:MG	H:null:HOH:O	1.839
D:null:MG:MG	H:null:HOH:O	1.839
C:null:MG:MG	H:null:HOH:O	1.839
G:null:MG:MG	H:null:HOH:O	1.839
D:null:MG:MG	H:null:HOH:O	1.84
B:null:MG:MG	H:null:HOH:O	1.84
F:null:MG:MG	H:null:HOH:O	1.84
C:null:MG:MG	H:null:HOH:O	1.84
C:null:MG:MG	H:null:HOH:O	1.84
C:null:MG:MG	H:null:HOH:O	1.84
G:null:MG:MG	H:null:HOH:O	1.84
D:null:MG:MG	H:null:HOH:O	1.84
B:null:MG:MG	H:null:HOH:O	1.84
G:null:MG:MG	H:null:HOH:O	1.84
E:null:MG:MG	H:null:HOH:O	1.84
F:null:MG:MG	H:null:HOH:O	1.84
B:null:MG:MG	H:null:HOH:O	1.841
D:null:MG:MG	H:null:HOH:O	1.841
G:null:MG:MG	H:null:HOH:O	1.841
C:null:MG:MG	H:null:HOH:O	1.841
G:null:MG:MG	H:null:HOH:O	1.841
F:null:MG:MG	H:null:HOH:O	1.841
B:null:MG:MG	H:null:HOH:O	1.841
E:null:MG:MG	H:null:HOH:O	1.842
D:null:MG:MG	H:null:HOH:O	1.842
E:null:MG:MG	H:null:HOH:O	1.842
A:30:A:OP1	B:null:MG:MG	2.337

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	MG	MAGNESIUM ION	None
B	2	MG	MAGNESIUM ION	None
B	3	MG	MAGNESIUM ION	None
B	4	MG	MAGNESIUM ION	None
B	5	MG	MAGNESIUM ION	None
B	6	MG	MAGNESIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40-------
GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG
|||||||||||||||||||||||||||||||||||||||||||||||
GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_25164_2mtk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	693		100.0 (chain: A, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1919 (1)	noe	100.0 (chain: A, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	160 (160)	.	93.6 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%

--------10--------20--------30--------40-------
GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG
|||||||||||||||||||||||||||||||||||||||||||||||
GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG

Total number of assignments
- ¹H chemical shifts: 368
- ¹³C chemical shifts: 286
- ¹⁵N chemical shifts: 39

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
4	C	N4	99.169
5	C	N4	98.567
7	C	N4	97.644
8	C	N4	98.281
9	C	N4	97.316
12	C	N4	99.207
13	C	N4	97.85
19	C	N4	98.802
21	G	H21	7.883
21	G	H22	7.093
21	G	N2	75.048
27	C	N4	98.935
29	A	H61	6.345
29	A	N6	78.928
30	A	H61	6.327
30	A	N6	80.579
33	C	N4	98.495
39	A	H61	6.101
39	A	N6	72.58
45	C	N4	98.662

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	413	363	87.9
¹³C chemical shifts	313	286	91.4
¹⁵N chemical shifts	27	24	88.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	282	239	84.8
¹³C chemical shifts	235	208	88.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	131	124	94.7
¹³C chemical shifts	78	78	100.0
¹⁵N chemical shifts	27	24	88.9

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	30	30	100.0
¹³C chemical shifts	30	30	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of restraints: 1919
- Weight of restraints: 1.0 (1919)
- Potential type of restraints: square-well-parabolic (1919)
- Range of distance target values: 1.87, 21.8 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 93.6%
- Total number of restraints: 160
- Total number of restraints per polymer type: 160
- Weight of restraints: 1.0 (160)
- Potential type of restraints: square-well-parabolic (160)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords VS ribozyme, Three-way junction, Base triple, NMR, Mg2+ ions

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Found 1 Document (0.395 seconds)

BMRB: 25164

Sample #1

Sample #2

Sample #3

Related entities 1. RNA (47-MER), : 1 : 1 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 4 contents Detail