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BMRB: 25220

2MVS

N6-Methyladenosine RNA

Authors

Lynch, S.R., Kool, E.

Assembly

RNA duplex

Entity

1. RNA duplex (polymer, Thiol state: not present), 10 monomers, 3173.967 × 2 Da Detail

GGXCUAGUCC

Total weight

6347.934 Da

Max. entity weight

3173.967 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.0 %, Completeness: 68.5 %, Completeness (bb): 56.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	68.5 % (102 of 149)	87.5 % (70 of 80)	40.0 % (24 of 60)	88.9 % (8 of 9)
Suger, PO4	56.5 % (61 of 108)	81.5 % (44 of 54)	20.0 % (9 of 45)	88.9 % (8 of 9)
Nucleobase	100.0 % (41 of 41)	100.0 % (26 of 26)	100.0 % (15 of 15)
Aromatic	100.0 % (35 of 35)	100.0 % (20 of 20)	100.0 % (15 of 15)

1. N-6 Methyl Adenosine RNA

GGXCUAGUCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
2	sodium chloride	natural abundance	100 mM
3	EDTA	natural abundance	0.1 mM
4	sodium phosphate	natural abundance	10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

Release date

2015-09-03

Citation

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification
Roost, C., Lynch, S.R., Batista, P.J., Qu, K., Chang, H.Y., Kool, E.T.
J. Am. Chem. Soc. (2015), 137, 2107-2115, PubMed 25611135 , DOI 10.1021/ja513080v , Abstract

Experiments performed 7 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

2 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

4 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
2	sodium chloride	natural abundance	100 mM
3	EDTA	natural abundance	0.1 mM
4	sodium phosphate	natural abundance	10 mM

7 2D 1H-31P COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	N-6 Methyl Adenosine RNA	natural abundance	0.2 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	0.1 mM
8	sodium phosphate	natural abundance	10 mM

NMR combined restraints 10 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25220_2mvs.nef
Input source #2: Coordindates	2mvs.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)
1:2:G:O3'	1:3:6MZ:P	unknown	unknown	n/a
1:3:6MZ:O3'	1:4:C:P	unknown	unknown	n/a
2:2:G:O3'	2:3:6MZ:P	unknown	unknown	n/a
2:3:6MZ:O3'	2:4:C:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	3	6MZ	N6-METHYLADENOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
2	13	6MZ	N6-METHYLADENOSINE-5'-MONOPHOSPHATE	Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): 1 vs Auth_asym_ID (model): 1
Entity_assembly_ID (NMR): 2 vs Auth_asym_ID (model): 2

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
1	1	10	0	0	100.0
2	2	10	0	0	100.0

Content subtype: combined_25220_2mvs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	120		100.0 (chain: 1, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_9	OK	249 (1)	noe	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
2	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	38 (1)	hbond	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	80 (80)	.	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	18 (18)	.	90.0 (chain: 1, length: 10), 90.0 (chain: 2, length: 10)
3	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	20 (20)	.	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
4	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	18 (18)	.	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
5	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	20 (20)	.	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
6	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	14 (14)	.	70.0 (chain: 1, length: 10), 70.0 (chain: 2, length: 10)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 83
  - ¹³C chemical shifts: 28
  - ³¹P chemical shifts: 9
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
3	6MZ

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	P	0.221
4	C	P	-0.431
5	U	P	-0.404
6	A	H61	7.706
6	A	H62	6.261
6	A	P	0.092
7	G	H21	8.505
7	G	H22	6.239
7	G	P	0.021
8	U	P	-0.82
9	C	P	-0.295
10	C	P	-0.082

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	70	87.5
¹³C chemical shifts	60	24	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	44	81.5
¹³C chemical shifts	45	9	20.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	15	15	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK
- Total number of restraints: 4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_9
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 249
- Weight of restraints: 1.0 (249)
- Potential type of restraints: square-well-parabolic (249)
- Range of distance target values: 2.9, 4.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_8
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
    - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 1.7, 3.2 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: 1
    - Chain_ID: 2
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 80
- Total number of restraints per polymer type: 80
- Weight of restraints: 1.0 (80)
- Potential type of restraints: square-well-parabolic (80)
- Dihedral angle restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 90.0%
    - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 90.0%
  - Total number of restraints: 18
  - Total number of restraints per polymer type: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: square-well-parabolic (18)
  - Dihedral angle restraints per residue
    - Chain_ID: 1
    - Chain_ID: 2
  - Saveframe: CNS/XPLOR_dihedral_6
    - Status: OK
    - Experiment type: .
    - Sequence coverage of experimental data
      - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
      - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
    - Total number of restraints: 20
    - Total number of restraints per polymer type: 20
    - Weight of restraints: 1.0 (20)
    - Potential type of restraints: square-well-parabolic (20)
    - Dihedral angle restraints per residue
      - Chain_ID: 1
      - Chain_ID: 2
    - Saveframe: CNS/XPLOR_dihedral_7
      - Status: OK
      - Experiment type: .
      - Sequence coverage of experimental data
        Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
        --------10 GGXCUAGUCC |||||||||| GGXCUAGUCC
        Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
        --------20 GGXCUAGUCC |||||||||| GGXCUAGUCC
      - Total number of restraints: 18
        Epsilon angle constraints: 18
      - Total number of restraints per polymer type: 18
        Nucleic acid: 18
      - Weight of restraints: 1.0 (18)
        Epsilon angle constraints: 1.0 (18)
      - Potential type of restraints: square-well-parabolic (18)
        Epsilon angle constraints: square-well-parabolic (18)
      - Dihedral angle restraints per residue
        Chain_ID: 1
        Chain_ID: 2
      - Saveframe: CNS/XPLOR_dihedral_4
        Status: OK
        Experiment type: .
        Sequence coverage of experimental data
        Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
        --------10 GGXCUAGUCC |||||||||| GGXCUAGUCC
        Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
        --------20 GGXCUAGUCC |||||||||| GGXCUAGUCC
        Total number of restraints: 20
        Chi angle constraints: 20
        Total number of restraints per polymer type: 20
        Nucleic acid: 20
        Weight of restraints: 1.0 (20)
        Chi angle constraints: 1.0 (20)
        Potential type of restraints: square-well-parabolic (20)
        Chi angle constraints: square-well-parabolic (20)
        Dihedral angle restraints per residue
        Chain_ID: 1
        Chain_ID: 2
        Saveframe: CNS/XPLOR_dihedral_2
        Status: OK
        Experiment type: .
        Sequence coverage of experimental data
        Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 70.0%
        --------10 GGXCUAGUCC || | || || GG.C.AG.CC
        Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 70.0%
        --------20 GGXCUAGUCC || | || || GG.C.AG.CC
        Total number of restraints: 14
        Undefined angle constraints: 14
        Total number of restraints per polymer type: 14
        Nucleic acid: 14
        Weight of restraints: 1.0 (14)
        Undefined angle constraints: 1.0 (14)
        Potential type of restraints: square-well-parabolic (14)
        Undefined angle constraints: square-well-parabolic (14)
        Dihedral angle restraints per residue
        Chain_ID: 1
        Chain_ID: 2

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Found 1 Document (0.402 seconds)

BMRB: 25220

Sample #1

Sample #2

Experiments performed 7 experiments Detail

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NMR combined restraints 10 contents Detail