BMRB Entry 25784

Name: NMR Assignment and structure of CssA Thermometer from Neisseria meningitidis
Published: 2016-07-26

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PDB ID: 2n6w
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25784
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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:

NMR Assignment and structure of CssA Thermometer from Neisseria meningitidis

Deposition date:

2015-08-28

Original release date:

2016-07-26

Authors:

Barnwal, Ravi; Godin, Kate; Varani, Gabriele

Citation:

Citation: Barnwal, Ravi; Loh, Edmund; Godin, Kate; Yip, Jordan; Lavender, Hayley; Tang, Christoph; Varani, Gabriele. "Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis" Nucleic Acids Res. 44, 9426-9437 (2016).
PubMed: 27369378

Assembly members:

Assembly members:
CssA_RNA_thermometer_(68-MER), polymer, 68 residues, 21654.873 Da.

Natural source:

Natural source: Common Name: b-proteobacteria Taxonomy ID: 487 Superkingdom: Bacteria Kingdom: not available Genus/species: Neisseria meningitidis

Experimental source:

Experimental source: Production method: in vitro transcription

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CssA_RNA_thermometer_(68-MER): GGAAUUUAUGAGUACGUAGA GUAUAAUUAGUCUUCGGACU UCCUUAUACUUAUAUACUUA UAGAUUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	31
15N chemical shifts	26
1H chemical shifts	287

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (68-MER)	1

Entities:

Entity 1, RNA (68-MER) 68 residues - 21654.873 Da.

1

G

A

U

A

U

G

2

A

G

U

A

C

G

U

A

G

A

3

G

U

A

U

A

U

A

G

4

U

C

U

C

G

A

C

U

5

U

C

U

A

U

A

C

U

6

U

A

U

A

U

A

C

U

A

7

U

A

G

A

U

C

Samples:

sample_1: CssA RNA thermometer (68-MER)0.4 – 1.1 mM; CssA RNA thermometer (68-MER), 13C/15N-uniformly labeled, 0.4 – 1.1 mM; CssA RNA thermometer (68-MER), 13C/15N-AU labeled, 0.4 – 1.1 mM; CssA RNA thermometer (68-MER), partially deuterated, 0.4 – 1.1 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.0; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
ARTSY	sample_1	isotropic	sample_conditions_1
ARTSY	sample_1	anisotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

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

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

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

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz
Agilent INOVA 900 MHz