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BMRB: 15331

2JRG

NMR SOLUTION STRUCTURE OF THE ANTICODON OF E.coli TRNA-VAL3 WITH 2 MODIFICATIONS (cmo5U34 M6A37)

Authors

Vendeix, F.A. P., Dziergowska, A., Gustilo, E.M., Graham, W.D., Sproat, B., Malkiewicz, A., Agris, P.F.

Assembly

(cmo5U34 M6A37)-ASL Val3

Entity

1. (cmo5U34 M6A37)-ASL Val3 (polymer, Thiol state: not present), 17 monomers, 5183.105 Da Detail

CCUCCCUXAC XAGGAGG

Formula weight

5183.105 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.2 %, Completeness: 72.4 %, Completeness (bb): 66.7 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	72.4 % (97 of 134)	72.4 % (97 of 134)
Suger, PO4	66.7 % (60 of 90)	66.7 % (60 of 90)
Nucleobase	84.1 % (37 of 44)	84.1 % (37 of 44)
Aromatic	96.9 % (31 of 32)	96.9 % (31 of 32)

1. RNA ASLval

CCUCCCUXAC XAGGAGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA 17mer	natural abundance	1.5 ~ 2.0 mM
2	H2O		90 %
3	D2O		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
4	RNA 17mer	natural abundance		1.5 ~ 2.0 mM
5	D2O			100 %

Release date

2007-07-25

Citation

Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding
Vendeix, F.A. P., Dziergowska, A., Gustilo, E.M., Graham, W.D., Sproat, B., Malkiewicz, A., Agris, P.F.
Biochemistry (2008), 47, 6117-6129, PubMed 18473483 , DOI 10.1021/bi702356j , Abstract

Related entities 1. (cmo5U34 M6A37)-ASL Val3, : 1 : 17 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15331_2jrg.nef
Input source #2: Coordindates	2jrg.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)
1:7:U:O3'	1:8:CM0:P	unknown	unknown	n/a
1:8:CM0:O3'	1:9:A:P	unknown	unknown	n/a
1:10:C:O3'	1:11:6MZ:P	unknown	unknown	n/a
1:11:6MZ:O3'	1:12:A:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	34	CM0	5-(CARBOXYMETHOXY) URIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	37	6MZ	N6-METHYLADENOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--30--------40---
CCUCCCUXACXAGGAGG
|||||||||||||||||
CCUCCCUXACXAGGAGG
--------10-------

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_15331_2jrg.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	122		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	564 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	28 (1)	hbond	58.8 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	125 (125)	.	100.0 (chain: A, length: 17)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 122
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
34	CM0
37	6MZ

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
39	G	H21	6.222
39	G	H22	8.282
40	G	H21	5.946
40	G	H22	8.049
41	A	H61	7.868
41	A	H62	6.652
42	G	H21	6.127
42	G	H22	8.531

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	134	97	72.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	60	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	37	84.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 564
- Weight of restraints: 1.0 (564)
- Potential type of restraints: square-well-parabolic (564)
- Range of distance target values: 1.57, 7.03 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - 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: 1.71, 3.08 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTICODON STEM LOOP, ASL, CMO5U, E.coli, M6A, N6-methyladenosine, RNA HAIRPIN, TRNA, TRNA DOMAIN, URIDINE 5-OXYACETIC ACID, Valine

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Found 1 Document (0.63 seconds)

BMRB: 15331

Sample #1

Sample #2

Related entities 1. (cmo5U34 M6A37)-ASL Val3, : 1 : 17 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 5 contents Detail