BMRB Entry 15857

Name: NMR solution structure of the d3&#039;-hairpin including EBS1 together with IBS1 of the group II intron Sc.ai5(gamma)
Published: 2009-10-13

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15857

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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 solution structure of the d3'-hairpin including EBS1 together with IBS1 of the group II intron Sc.ai5(gamma)

Deposition date:

2008-07-04

Original release date:

2009-10-13

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_(29-MER), polymer, 29 residues, Formula weight is not available
RNA_(7-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: in vitro transcription Host organism: Saccharomyces cerevisiae

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(29-MER): GGAGUAUGUAUUGGCACUGA GCAUACUCC
RNA_(7-MER): CAGUGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	77
15N chemical shifts	13
1H chemical shifts	306

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (29-MER)	1
2	RNA (7-MER)	2

Entities:

Entity 1, RNA (29-MER) 29 residues - Formula weight is not available

1

G

A

G

U

A

U

G

U

A

2

U

G

C

A

C

U

G

A

3

G

C

A

U

A

C

U

C

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

1

C

A

G

U

G

U

C

Samples:

sample_1: RNA (29-MER) 0.5-0.9 mM; RNA (7-MER) 0.5-0.9 mM; potassium chloride 110 mM; EDTA 10 uM; MgCl2 0-10 mM; D2O, [U-100% 2H], 100%

sample_2: RNA (29-MER) 0.5-0.9 mM; RNA (7-MER) 0.5-0.9 mM; potassium chloride 110 mM; EDTA 10 uM; MgCl2 0-8 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_3: RNA (29-MER), [selectively deuterated at 3',4',5',5'',5], 0.6 mM; RNA (7-MER) 0.6 mM; potassium chloride 110 mM; EDTA 10 uM; D2O, [U-100% 2H], 100%

sample_4: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.5 mM; RNA (7-MER) 0.5 mM; potassium chloride 50 mM; EDTA 10 uM; H2O 90%; D2O, [U-100% 2H], 10%

sample_5: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.5 mM; RNA (7-MER) 0.5 mM; potassium chloride 50 uM; EDTA 10 uM; Pf1 phage 25.6 mg/ml; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 115 mM; pD: 6.8; pressure: 1 atm; temperature: 288 K

sample_conditions_5: ionic strength: 115 mM; pD: 6.8; pressure: 1 atm; temperature: 293 K

sample_conditions_6: ionic strength: 115 mM; pD: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_7: ionic strength: 1105 mM; pD: 6.8; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 114 mM; pH: 6.65; pressure: 1 atm; temperature: 278 K

sample_conditions_8: ionic strength: 114 mM; pH: 6.65; pressure: 1 atm; temperature: 293 K

sample_conditions_3: ionic strength: 110 mM; pD: 6.6; pressure: 1 atm; temperature: 298 K

sample_conditions_4: ionic strength: 10 mM; pH: 6.6; pressure: 1 atm; temperature: 278 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-1H NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_4
2D 1H-13C HSQC	sample_5	anisotropic	sample_conditions_3
2D 1H-15N HSQC	sample_5	anisotropic	sample_conditions_4
2D JNN HNN-COSY	sample_4	isotropic	sample_conditions_4
3D X filtered NOESY-15NHSQC	sample_4	isotropic	sample_conditions_4
2D X filtered NOESY	sample_4	isotropic	sample_conditions_3
2D X filtered TOCSY	sample_4	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