BMRB Entry 18549

Name: Solution Structure of Helix-35 Stem-loop from E. coli 23S rRNA
Published: 2013-06-24

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PDB ID: 2lv0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18549
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of Helix-35 Stem-loop from E. coli 23S rRNA

Deposition date:

2012-06-26

Original release date:

2013-06-24

Authors:

Nikonowicz, Edward; Wang, Jiachen; Moran, Sean; Donarski, James

Citation:

Citation: Moran, Sean; Donarski, James; Wang, Jiachen; Nikonowicz, Edward. "Solution Structure of Helix-35 Stem-loop from E. coli 23S rRNA" .

Assembly members:

Assembly members:
RNA, polymer, 24 residues, 132.116 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA: GGGCUAAUGUUGAAAAAUUA GCCC

Data sets:

assigned_chemical_shifts
- D2Ochemshifts

Data type	Count
13C chemical shifts	181
15N chemical shifts	42
1H chemical shifts	185

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1

Entities:

Entity 1, RNA 24 residues - 132.116 Da.

1

G

C

U

A

U

G

U

2

U

G

A

U

A

3

G

C

Samples:

CN_D2O: RNA, [U-99% 13C; U-99% 15N], 1.2 ± 0.1 mM; potassium phosphate 10 ± 1.0 mM; sodium chloride 10 ± 1.0 mM; EDTA 0.1 ± 0.5 mM; D2O 100%

NatAb_D2O: RNA 1.6 ± 0.1 mM; potassium phosphate 10 ± 1.0 mM; sodium chloride 10 ± 1.0 mM; EDTA 0.1 ± 0.5 mM; D2O 100%

NatAb_H2O: RNA 1.6 ± 0.1 mM; potassium phosphate 10 ± 1.0 mM; sodium chloride 10 ± 1.0 mM; EDTA 0.1 ± 0.5 mM; D2O 10%; H2O 90%

CN_H2O: RNA, [U-99% 13C; U-99% 15N], 1.2 ± 0.1 mM; potassium phosphate 10 ± 1.0 mM; sodium chloride 10 ± 1.0 mM; EDTA 0.1 ± 0.5 mM; D2O 10%; H2O 90%

25C: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

10C: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	CN_H2O	isotropic	10C
2D 1H-13C HSQC	CN_D2O	isotropic	25C
3D HCCH-TOCSY	CN_D2O	isotropic	25C
3D 1H-13C NOESY	CN_D2O	isotropic	25C
2D 1H-1H NOESY	NatAb_D2O	isotropic	25C
2D DQF-COSY	NatAb_D2O	isotropic	25C
2D 1H-1H NOESY	NatAb_H2O	isotropic	10C
3D HCCH-COSY	CN_D2O	isotropic	25C
2D 1H-31P HetCor	NatAb_D2O	isotropic	25C
2D 1H-15N HMQC	CN_D2O	isotropic	25C
2D 1H-13C ctHSQC-31P	CN_D2O	isotropic	25C
2D 1H-15N HCN	CN_D2O	isotropic	25C
3D 1H-15N NOESY	CN_H2O	isotropic	10C

Software:

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

FELIX, Accelrys Software Inc. - processing, refinement

VNMR, Varian - collection, refinement

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz