BMRBj - BMREntryMaster

Found 1 Document (0.326 seconds)

BMRB: 18239

2LP9

Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus

Authors

Skov, J.

Assembly

RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3')

Entity

1. RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3') (polymer, Thiol state: not present), 16 monomers, 5185.075 Da Detail

GAGGACAUAG AUCUUC

Formula weight

5185.075 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 76.6 %, Completeness (bb): 70.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	³¹P
All	76.6 % (118 of 154)	74.6 % (103 of 138)	93.8 % (15 of 16)
Suger, PO4	70.5 % (79 of 112)	66.7 % (64 of 96)	93.8 % (15 of 16)
Nucleobase	92.9 % (39 of 42)	92.9 % (39 of 42)
Aromatic	97.2 % (35 of 36)	97.2 % (35 of 36)

1. RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3')

GAGGACAUAG AUCUUC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 2 mM RNA, 10 mM sodium phosphate buffer (pH 7), 50 mM NaCl, 2 mM EDTA

#	Name	Isotope labeling	Concentration
1	wt_RNA	natural abundance	2 mM
2	sodium phosphate	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	EDTA	natural abundance	2 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Release date

2012-03-11

Citation

The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter
Skov, J., Gaudin, M., Podbevsek, P., Olsthoorn, R.C.L., Petersen, M.
RNA (2012), 18, 992-1000, PubMed 22393035 , DOI 10.1261/rna.029918.111 , Abstract

Related entities 1. RNA (5'-R(GPAPGPGPAPCPAPUPAPGPAPUPCPUPUPC)-3'), : 1 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18239_2lp9.nef
Input source #2: Coordindates	2lp9.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10------
GAGGACAUAGAUCUUC
||||||||||||||||
GAGGACAUAGAUCUUC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	16	0	0	100.0

Content subtype: combined_18239_2lp9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	120		100.0 (chain: A, length: 16)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	238 (1)	noe	100.0 (chain: A, length: 16)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	19 (1)	noe	50.0 (chain: A, length: 16)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	15 (1)	hbond	75.0 (chain: A, length: 16)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	126 (126)	.	100.0 (chain: A, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 105
  - ³¹P chemical shifts: 15
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	A	P	-3.96
3	G	P	-4.25
4	G	H22	8.44
4	G	H21	6.46
4	G	P	-3.86
5	A	P	-3.82
6	C	P	-3.5
7	A	P	-3.88
8	U	P	-4.1
9	A	P	-3.8
10	G	P	-4.09
11	A	P	-4.38
12	U	P	-4.26
13	C	P	-3.47
14	U	P	-3.75
15	U	P	-2.79
16	C	P	-3.64

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	138	103	74.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	64	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	39	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
- Total number of restraints: 238
- Weight of restraints: 1.0 (238)
- Potential type of restraints: square-well-parabolic (238)
- Range of distance target values: 2.4, 5.0 (Å)
- Histogram of 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: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 50.0%
  - Total number of restraints: 19
  - Weight of restraints: 1.0 (19)
  - Potential type of restraints: square-well-parabolic (19)
  - Range of distance target values: 4.0, 5.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 75.0%
    - Total number of restraints: 15
    - Weight of restraints: 1.0 (15)
    - Potential type of restraints: square-well-parabolic (15)
    - Range of distance target values: 1.92, 1.92 (Å)
    - 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: 16, Sequence coverage: 100.0%
- Total number of restraints: 126
- Total number of restraints per polymer type: 126
- Weight of restraints: 1.0 (126)
- Potential type of restraints: square-well-parabolic (126)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Brome Mosaic Virus, NMR spectroscopy, pseudo-triloop, RNA replication

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Found 1 Document (0.326 seconds)

BMRB: 18239

Sample

Related entities 1. RNA (5'-R(GPAPGPGPAPCPAPUPAPGPAPUPCPUPUPC)-3'), : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.326 seconds)

BMRB: 18239

Sample

Related entities 1. RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3'), : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail

Related entities 1. RNA (5'-R(GPAPGPGPAPCPAPUPAPGPAPUPCPUPUPC)-3'), : 1 entities Detail