BMRBj - BMREntryMaster

Found 1 Document (1.098 seconds)

BMRB: 17573

2LBR

Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR

Authors

Denmon, A.P., Wang, J., Nikonowicz, E.P.

Assembly

Anticodon Stem-loop (coi6y)

Entity

1. Anticodon Stem-loop (coi6y) (polymer, Thiol state: not present), 17 monomers, 5575.406 Da Detail

GGGGACUGUA XAXCCCC

Formula weight

5575.406 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.2 %, Completeness: 35.3 %, Completeness (bb): 20.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	35.3 % (82 of 232)	36.4 % (48 of 132)	34.0 % (34 of 100)
Suger, PO4	20.0 % (33 of 165)	25.6 % (23 of 90)	13.3 % (10 of 75)
Nucleobase	73.1 % (49 of 67)	59.5 % (25 of 42)	96.0 % (24 of 25)
Aromatic	86.0 % (49 of 57)	78.1 % (25 of 32)	96.0 % (24 of 25)

1. coi6y

GGGGACUGUA XAXCCCC

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	i6A,PSU-ASL	natural abundance	2.0 mM
2	potassium chloride	natural abundance	10 mM
3	EDTA	natural abundance	0.02 mM
4	potassium phosphate	natural abundance	10 mM
5	D2O	natural abundance	100 %

Release date

2011-08-01

Citation

Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr)
Denmon, A.P., Wang, J., Nikonowicz, E.P.
J. Mol. Biol. (2011), 412, 285-303, PubMed 21782828 , DOI 10.1016/j.jmb.2011.07.010 , Abstract

Related entities 1. Anticodon Stem-loop (coi6y), : 1 : 2 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17573_2lbr.nef
Input source #2: Coordindates	2lbr.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)
1:10:A:O3'	1:11:6IA:P	unknown	unknown	n/a
1:11:6IA:O3'	1:12:A:P	unknown	unknown	n/a
1:12:A:O3'	1:13:PSU:P	unknown	unknown	n/a
1:13:PSU:O3'	1:14:C:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	11	6IA	N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	13	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-------
GGGGACUGUAXAXCCCC
|||||||||||||||||
GGGGACUGUAXAXCCCC

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_17573_2lbr.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	111		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	285 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	28 (1)	hbond	58.8 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	121 (121)	.	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: 73
  - ¹³C chemical shifts: 38
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
11	6IA

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	HO2'	4.4
2	G	HO2'	4.59
3	G	HO2'	4.59
4	G	HO2'	4.48
5	A	HO2'	4.58
6	C	HO2'	4.4
7	U	HO2'	4.26
10	A	HO2'	4.89
12	A	HO2'	4.27
14	C	HO2'	4.24
15	C	HO2'	4.35
16	C	HO2'	4.39
17	C	HO2'	4.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	144	51	35.4
¹³C chemical shifts	109	35	32.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	25	25.8
¹³C chemical shifts	80	10	12.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	26	55.3
¹³C chemical shifts	29	25	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	11	10	90.9

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- 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: 285
- Weight of restraints: 1.0 (285)
- Potential type of restraints: square-well-parabolic (285)
- Range of distance target values: 2.4, 6.25 (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_4
  - 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: 2.1, 3.05 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 121
- Total number of restraints per polymer type: 121
- Weight of restraints: 1.0 (121)
- Potential type of restraints: square-well-parabolic (121)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords i6A, Psu, Tyrosyl-tRNA

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Found 1 Document (1.098 seconds)

BMRB: 17573

Sample

Related entities 1. Anticodon Stem-loop (coi6y), : 1 : 2 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail