BMRB Entry 30108

Name: Solution structures of the apo state fluoride riboswitch
Published: 2017-07-14

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PDB ID: 5kh8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30108
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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:

Solution structures of the apo state fluoride riboswitch

Deposition date:

2016-06-14

Original release date:

2017-07-14

Authors:

Zhang, Q.; Zhao, B.

Citation:

Citation: Zhao, Bo; Guffy, Sharon; Williams, Benfeard; Zhang, Qi. "An excited state underlies gene regulation of a transcriptional riboswitch" Nat. Chem. Biol. 13, 968-974 (2017).
PubMed: 28719589

Assembly members:

Assembly members:
riboswitch (47-MER), polymer, 47 residues, 15053.960 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
riboswitch (47-MER): GGCGAUGGUGUUCGCCAUAA ACGCUCUUCGGAGCUAAUGA CACCUAC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	240
15N chemical shifts	19
1H chemical shifts	289

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 47 residues - 15053.960 Da.

1

G

C

G

A

U

G

U

G

2

U

C

G

C

A

U

A

3

A

C

G

C

U

C

U

C

G

4

G

A

G

C

U

A

U

G

A

5

C

A

C

U

A

C

Samples:

sample_1: EDTA 50 uM; RNA (47mer) 1.0 mM; magnesium chloride 10 mM; potassium chloride 50 mM; sodium phosphate 10 mM; H2O 95%; D2O 5%

sample_2: EDTA 50 uM; RNA (47mer) 1.0 mM; magnesium chloride 10 mM; potassium chloride 50 mM; sodium phosphate 10 mM; D2O 100%

sample_3: EDTA 50 uM; RNA (47mer), [U-100% 13C; U-100% 15N], 1.0 mM; magnesium chloride 10 mM; potassium chloride 50 mM; sodium phosphate 10 mM; H2O 95%; D2O 5%

sample_4: EDTA 50 uM; RNA (47mer), [U-100% 13C; U-100% 15N], 1.0 mM; magnesium chloride 10 mM; potassium chloride 50 mM; sodium phosphate 10 mM; D2O 100%

sample_5: EDTA 50 uM; RNA (47mer), [U-13C; U-15N]-Gua, 1.0 mM; magnesium chloride 10 mM; potassium chloride 50 mM; sodium phosphate 10 mM; D2O 100%

sample_6: EDTA 50 uM; RNA (47mer), [U-13C; U-15N]-Ade ;[U-13C; U-15N]-Ura, 1.0 mM; magnesium chloride 10 mM; potassium chloride 50 mM; sodium phosphate 10 mM; D2O 100%

sample_conditions_1: ionic strength: 80 mM; pH: 6.4; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 80 mM; pH: 6.4; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D HCCH COSY	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_6	isotropic	sample_conditions_1
2D HCCH COSY	sample_6	isotropic	sample_conditions_1
31P spin-echo	sample_6	isotropic	sample_conditions_1
31P spin-echo	sample_5	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	anisotropic	sample_conditions_1
CH-HCCH spin-echo	sample_5	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	anisotropic	sample_conditions_1
CH-HCCH spin-echo	sample_6	isotropic	sample_conditions_1

Software:

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, processing

SPARKY v3.110, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN v3.2, Bruker Biospin - collection, data analysis, processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 500 MHz