BMRB Entry 17564

Name: Glycyl-tRNA(UCC)1B anticodon stem-loop from Staphylococcus epidermidis
Published: 2012-04-04

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PDB ID: 2lbk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17564
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Glycyl-tRNA(UCC)1B anticodon stem-loop from Staphylococcus epidermidis

Deposition date: 2011-03-31 Original release date: 2012-04-04

Authors: Chang, Andrew; Nikonowicz, Edward

Citation: Chang, Andrew; Nikonowicz, Edward. "Structure solution of three glycyl-tRNA anticodon stem-loop" Not known ., .-..

Assembly members:
Glycyl-tRNA(UCC)1B anticodon stem-loop, polymer, 17 residues, 5371.249 Da.

Natural source: Common Name: S. epidermidis Taxonomy ID: 1282 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus epidermidis

Experimental source: Production method: enzymatic semisynthesis Host organism: Staphylococcus epidermidis

Entity Sequences (FASTA):
Glycyl-tRNA(UCC)1B anticodon stem-loop: GGGACCUUCCCGGUCUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	87
1H chemical shifts	107

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Glycyl-tRNA(UCC)1B anticodon stem-loop	1

Entities:

Entity 1, Glycyl-tRNA(UCC)1B anticodon stem-loop 17 residues - 5371.249 Da.

1

G

A

C

U

C

2

C

G

U

C

U

C

Samples:

sample_1: RNA0.02 – 0.04 mM; D2O 100%; KH2PO4 10 mM; K2HPO4 10 mM; KCl 10 mM; EDTA 0.2 mM; MgCl2 10 mM

sample_2: RNA0.02 – 0.04 mM; H2O 90%; D2O 10%; KH2PO4 10 mM; K2HPO4 10 mM; KCl 10 mM; EDTA 0.2 mM; MgCl2 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D HCN	sample_1	isotropic	sample_conditions_1

Software:

FELIX, Accelrys Software Inc. - chemical shift assignment, processing

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

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz