BMRB Entry 17877

Name: Solution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch
Published: 2012-08-22

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PDB ID: 2li4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17877
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch PubMed: 22976989

Deposition date: 2011-08-22 Original release date: 2012-08-22

Authors: Korth, Maximiliane; Sigel, Roland

Citation: Korth, Maximiliane; Sigel, Roland. "Unusually high-affinity Mg(2+) binding at the AU-rich sequence within the antiterminator hairpin of a Mg(2+) riboswitch." Chem. Biodivers. 9, 2035-2049 (2012).

Assembly members:
RNA_(32-MER), polymer, 32 residues, 10304.251 Da.

Natural source: Common Name: Yersinia enterocolitica Taxonomy ID: 630 Superkingdom: Bacteria Kingdom: not available Genus/species: Yersinia enterocolitica

Experimental source: Production method: cell free synthesis

Entity Sequences (FASTA):
RNA_(32-MER): GGACCGAUAAGGUAGAAAUG CCUUAUCGGUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	232

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (32-MER)	1

Entities:

Entity 1, RNA (32-MER) 32 residues - 10304.251 Da.

1

G

A

C

G

A

U

A

2

G

U

A

G

A

U

G

3

C

U

A

U

C

G

U

4

C

Samples:

sample_1: potassium chloride 50 mM; EDTA 10 uM; RNA (32-MER) 0.24 mM; D2O 100%

sample_2: potassium chloride 50 mM; EDTA 10 uM; RNA (32-MER) 0.6 mM; D2O 10%; H2O 90%

sample_3: potassium chloride 50 mM; EDTA 10 uM; RNA (32-MER) 0.8 mM; D2O 100%

sample_4: potassium chloride 50 mM; EDTA 10 uM; RNA (32-MER) 0.5 mM; D2O 100%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.8; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 0.05 M; pH: 6.8; pressure: 1 atm; temperature: 278 K

sample_conditions_3: ionic strength: 0.05 M; pH: 6.8; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_3

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

SPARKY v3.1, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN v1.3, 2.1, 3.0a, Bruker Biospin - processing

X-PLOR v2.24, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker Avance 700 MHz