BMRB Entry 19698

Name: Solution NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae
Published: 2014-01-27

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PDB ID: 2miy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19698
MolProbity Validation Chart

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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 NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae

Deposition date:

2013-12-20

Original release date:

2014-01-27

Authors:

Kang, Mijeong; Eichhorn, Catherine; Feigon, Juli

Citation:

Citation: Kang, Mijeong; Eichhorn, Catherine; Feigon, Juli. "Structural determinants for ligand capture by a class II preQ1 riboswitch." Proc. Natl. Acad. Sci. U.S.A. 111, E663-E671 (2014).
PubMed: 24469808

Assembly members:

Assembly members:
RNA_(59-MER), polymer, 59 residues, 18903.389 Da.
7-DEAZA-7-AMINOMETHYL-GUANINE, non-polymer, 179.179 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: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(59-MER): GCUUGGUGCUUAGCUUCUUU CACCAAGCAUAUUACACGCG GAUAACCGCCAAAGGAGAA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	399
15N chemical shifts	20
1H chemical shifts	620

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (59-MER)	1
2	7-DEAZA-7-AMINOMETHYL-GUANINE	2

Entities:

Entity 1, RNA (59-MER) 59 residues - 18903.389 Da.

1

G

C

U

G

U

G

C

U

2

U

A

G

C

U

C

U

3

C

A

C

A

G

C

A

U

4

A

U

A

C

A

C

G

C

G

5

G

A

U

A

C

G

C

6

A

G

A

G

A

Entity 2, 7-DEAZA-7-AMINOMETHYL-GUANINE - 179.179 Da.

1

PRF

Samples:

sample_1: RNA (59-MER)1.0 – 1.2 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; potassium chloride 60 mM; calcium chloride 3 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_2: RNA (59-MER)1.0 – 1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_3: RNA (59-MER), [U-50% 2H, 0.8 – 1.0 mM; potassium chloride 60 mM; calcium Chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_4: RNA (59-MER), [U-13C; U-15N]-Ade, 1.0 – 1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_5: RNA (59-MER), [U-13C; U-15N]-Gua, 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_6: RNA (59-MER), [U-13C; U-15N]-Cyt, 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_7: RNA (59-MER), [U-13C; U-15N]-Ura, 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_8: RNA (59-MER), [U-100% 13C; U-100% 15N], 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 66 mM; pH: 6.15; pressure: 1 atm; temperature: 300 K

sample_conditions_2: ionic strength: 66 mM; pH: 6.15; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_5	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_7	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_8	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_8	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, data analysis

xwinnmr, Bruker Biospin - collection, processing

TOPSPIN, Bruker Biospin - collection, processing

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRDraw, Johnson, One Moon Scientific - peak picking

InsightII, Accelrys Software Inc. - data analysis

NMR spectrometers:

Bruker DRX 600 MHz
Bruker Avance 800 MHz