BMRB Entry 16604

Name: 1H, 13C, 15N chemical shift sssignments of the artificial neomycin-sensing riboswitch in complex with tobramycin
Published: 2010-09-02

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16604

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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:

1H, 13C, 15N chemical shift sssignments of the artificial neomycin-sensing riboswitch in complex with tobramycin

Deposition date:

2009-11-11

Original release date:

2010-09-02

Authors:

Schmidtke, Sina; Duchardt-Ferner, Elke; Weigand, Julia; Suess, Beatrix; Woehnert, Jens

Citation:

Citation: Schmidtke, Sina; Duchardt-Ferner, Elke; Weigand, Julia; Suess, Beatrix; Woehnert, Jens. "NMR resonance assignments of an engineered neomycin-sensing riboswitch RNA bound to ribostamycin and tobramycin" Biomol. NMR Assign. 4, 115-118 (2010).
PubMed: 20306311

Assembly members:

Assembly members:
Neo-Riboswitch, polymer, 27 residues, 467.514 Da.
TOY, non-polymer, 467.514 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: in vitro transcription Host organism: Saccharomyces cerevisiae

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Neo-Riboswitch: GGCUGCUUGUCCUUUAAUGG UCCAGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	174
15N chemical shifts	49
1H chemical shifts	235

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1
2	Aminoglycoside	2

Entities:

Entity 1, RNA 27 residues - 467.514 Da.

1

G

C

U

G

C

U

G

U

2

C

U

A

U

G

3

U

C

A

G

U

C

Entity 2, Aminoglycoside - C18 H37 N5 O9 - 467.514 Da.

1

TOY

Samples:

sample_1: Neo-Aptamer 1.1 mM; Tobramycin 1.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; H2O 90%; D2O 10%

sample_2: Neo-Aptamer, [U-13C; U-15N], 1.1 mM; Tobramycin 1.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; H2O 90%; D2O 10%

sample_3: Neo-Aptamer, [U-13C; U-15N], 1.1 mM; Tobramycin 1.2 mM; potassium chloride 50 mM; potassium phosphate 25 mM; D2O 100%

sample_4: Neo-Aptamer, [U-13C; U-15N]-Ura-Ade, 1.2 mM; Tobramycin 1.3 mM; potassium chloride 50 mM; potassium phosphate 25 mM; D2O 100%

condition_1: pH: 6.2; pressure: 1 atm; temperature: 283 K

condition_2: pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H-HS11ECHO	sample_1	isotropic	condition_1
2D 1H-1H NOESY	sample_1	isotropic	condition_1
2D 1H-15N HSQC	sample_2	isotropic	condition_1
2D 1H-15N-HNN-COSY	sample_2	isotropic	condition_1
2D 1H-13C-HNCO	sample_2	isotropic	condition_1
2D 1H-13C H5(6)C5(6)C4N3H	sample_2	isotropic	condition_1
2D 1H-15N HCN	sample_3	isotropic	condition_1
2D 1H-13C HSQC	sample_2	isotropic	condition_1
2D 1H-13C HSQC	sample_3	isotropic	condition_2
3D HCCH-COSY	sample_3	isotropic	condition_2
3D HCCH-TOCSY	sample_3	isotropic	condition_2
3D 1H-1H NOESY-HSQC	sample_3	isotropic	condition_2
3D 1H-1H NOESY-HMQC	sample_3	isotropic	condition_2
2D 1H-1H HCCH-TOCSY (Adenine)	sample_3	isotropic	condition_2
3D 1H-1H NOESY-HMQC	sample_4	isotropic	condition_2
2D 1H-13C HSQC	sample_4	isotropic	condition_2

Software:

TOPSPIN v2.1, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz
Bruker Avance 950 MHz