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BMRB: 17517

2LA9

Pseudouridine_ASL_Tyr

Authors

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

Assembly

Anticodon Stem-loop of Bacillus subtilis tRNATYR

Entity

1. Anticodon Stem-loop of Bacillus subtilis tRNATYR (polymer, Thiol state: not present), 17 monomers, 5505.273 Da Detail

GGGGACUGUA AAXCCCC

Formula weight

5505.273 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 41.8 %, Completeness (bb): 33.9 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	41.8 % (110 of 263)	43.6 % (61 of 140)	31.8 % (34 of 107)	93.8 % (15 of 16)
Suger, PO4	33.9 % (65 of 192)	36.5 % (35 of 96)	18.8 % (15 of 80)	93.8 % (15 of 16)
Nucleobase	63.4 % (45 of 71)	59.1 % (26 of 44)	70.4 % (19 of 27)
Aromatic	73.8 % (45 of 61)	76.5 % (26 of 34)	70.4 % (19 of 27)

1. tRNATYR

GGGGACUGUA AAXCCCC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Pseudouridine_ASL_Tyr	natural abundance	2.0 mM
2	potassium chloride	natural abundance	10 mM
3	potassium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.02 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

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

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 17520 released on 2011-08-01
    Title Unmodified_ASL_Tyr
  BMRB: 17572 released on 2011-08-01
    Title i6A37_tyrASL
  BMRB: 17573 released on 2011-08-01
    Title Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR

Related entities 1. Anticodon Stem-loop of Bacillus subtilis tRNATYR, : 1 : 3 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17517_2la9.nef
Input source #2: Coordindates	2la9.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)
1:12: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	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-------
GGGGACUGUAAAXCCCC
|||||||||||||||||
GGGGACUGUAAAXCCCC

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_17517_2la9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	131		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	278 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	42 (1)	hbond	70.6 (chain: A, length: 17)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	3 (1)	hbond	11.8 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	135 (135)	.	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: 80
- ¹³C chemical shifts: 35
- ³¹P chemical shifts: 16

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	HO2'	4.59
2	G	P	-3.76
3	G	HO2'	4.61
3	G	P	-3.57
4	G	HO2'	4.6
4	G	P	-3.54
5	A	HO2'	4.59
5	A	P	-3.87
6	C	HO2'	4.58
6	C	P	-4.24
7	U	HO2'	4.22
7	U	P	-3.95
8	G	HO2'	4.57
8	G	P	-3.7
9	U	HO2'	4.14
9	U	P	-3.67
10	A	HO2'	4.44
10	A	P	-3.88
11	A	HO2'	4.51
11	A	P	-3.46
12	A	P	-3.86
14	C	P	-4.24
15	C	HO2'	4.34
15	C	P	-4.4
16	C	HO2'	4.24
16	C	P	-4.3
17	C	HO2'	3.98
17	C	P	-4.15

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	152	67	44.1
¹³C chemical shifts	116	35	30.2
³¹P chemical shifts	1	1	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	40	38.8
¹³C chemical shifts	85	15	17.6
³¹P chemical shifts	1	1	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	27	55.1
¹³C chemical shifts	31	20	64.5

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	13	12	92.3
¹³C chemical shifts	13	12	92.3

Histogram of normalized assigned chemical shifts

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: 278
- Weight of restraints: 1.0 (278)
- Potential type of restraints: square-well-parabolic (278)
- Range of distance target values: 2.4, 14.4 (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_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 70.6%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: square-well-parabolic (42)
  - Range of distance target values: 2.0, 9.9 (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: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 11.8%
    - Total number of restraints: 3
    - Weight of restraints: 1.0 (3)
    - Potential type of restraints: square-well-parabolic (3)
    - Range of distance target values: 4.25, 4.25 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - 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: 17, Sequence coverage: 100.0%
- Total number of restraints: 135
- Total number of restraints per polymer type: 135
- Weight of restraints: 1.0 (135)
- Potential type of restraints: square-well-parabolic (135)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Pseudouridine, Tyrosyl-tRNA

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Found 1 Document (0.439 seconds)

BMRB: 17517

Sample

Entries sharing articles BMRB: 3 entries Detail

Related entities 1. Anticodon Stem-loop of Bacillus subtilis tRNATYR, : 1 : 3 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail