BMRB Entry 30224

Name: Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator
Published: 2017-05-25

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PDB ID: 5uf3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30224
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator

Deposition date:

2017-01-03

Original release date:

2017-05-25

Authors:

Chang, A.; Tran, M.; DeJong, E.; Nikonowicz, E.

Citation:

Citation: Chang, A.; Tran, M.; Nikonowicz, E.. "Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator" Biochemistry 56, 2690-2700 (2017).
PubMed: 28488852

Assembly members:

Assembly members:
phage GA operator RNA hairpin, polymer, 23 residues, 7394.496 Da.

Natural source:

Natural source: Common Name: Enterobacteria phage GA Taxonomy ID: 12018 Superkingdom: Viruses Kingdom: not available Genus/species: Levivirus Escherichia virus BZ13

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
phage GA operator RNA hairpin: GGACAUAAGGAAAACCUAUG UCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	158
15N chemical shifts	49
1H chemical shifts	196
31P chemical shifts	21

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 23 residues - 7394.496 Da.

1

G

A

C

A

U

A

G

2

A

C

U

A

U

G

3

U

C

Samples:

sample_4: Pf1 phage 15 mg/mL; phage GA operator RNA hairpin, [U-13C; U-15N], 0.3 ± 0.01 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%

sample_5: EDTA 0.02 mM; phage GA operator RNA hairpin, 2H, 40%-85%, 1.2 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%

sample_6: EDTA 0.02 mM; phage GA operator RNA hairpin, 13C, 4%-20%, 1.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%

sample_1: EDTA 0.02 mM; phage GA operator RNA hairpin, [U-13C; U-15N], 1 ± 0.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%

sample_2: EDTA 0.02 mM; phage GA operator RNA hairpin 1.5 ± 0.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O 100%

sample_3: EDTA 0.02 mM; phage GA operator RNA hairpin, [U-13C; U-15N], 1 ± 0.1 mM; potassium chloride 10 mM; potassium phosphate 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 285 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-31P HetCor	sample_5	isotropic	sample_conditions_1
2D 1H-13C CTEP	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_6	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	anisotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-13C H(N)CO	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C H(CN)CO	sample_1	isotropic	sample_conditions_1
2D 1H-13C C(C)H-COSY	sample_1	isotropic	sample_conditions_1

Software:

Felix, Accelrys Software Inc. - processing

X-PLOR NIH v2.43, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz