BMRB Entry 15858

Name: NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma)
Published: 2009-10-12

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PDB ID: 2k65
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15858
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma)

Deposition date:

2008-07-04

Original release date:

2009-10-12

Authors:

Kruschel, Daniela; Sigel, Roland

Citation:

Citation: Kruschel, Daniela; Sigel, Roland. "Solution structure of the 5'-splice site of a group II intron ribozyme" .

Assembly members:

Assembly members:
RNA_(7A-MER), polymer, 7 residues, Formula weight is not available
RNA_(7B-MER), polymer, 7 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(7A-MER): GGCACUG
RNA_(7B-MER): CAGUGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	36
1H chemical shifts	117

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (7A-MER)	1
2	RNA (7B-MER)	2

Entities:

Entity 1, RNA (7A-MER) 7 residues - Formula weight is not available

1

G

C

A

C

U

G

Entity 2, RNA (7B-MER) 7 residues - Formula weight is not available

1

C

A

G

U

G

U

C

Samples:

sample_1: RNA (7A-MER) 0.8-0.9 mM; RNA (7B-MER) 0.8-0.9 mM; potassium chloride 100 mM; EDTA 10 uM; D2O, [U-100% 2H], 100%

sample_2: RNA (7A-MER) 0.9 mM; RNA (7B-MER) 0.9 mM; potassium chloride 100 mM; EDTA 10 uM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 100 mM; pD: 6.7; pressure: 1 atm; temperature: 288 K

sample_conditions_4: ionic strength: 100 mM; pD: 6.7; pressure: 1 atm; temperature: 293 K

sample_conditions_5: ionic strength: 100 mM; pD: 6.7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.3; pressure: 1 atm; temperature: 278 K

sample_conditions_3: ionic strength: 100 mM; pD: 6.7; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_3

Software:

TOPSPIN v1.3, 2.0, 2.1, Bruker Biospin - processing

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

DYANA v1.5, Guntert, Braun and Wuthrich - structure solution

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

X-PLOR NIH v2.16, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 700 MHz