BMRB Entry 34199

Name: Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding
Published: 2018-01-12

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PDB ID: 6ez0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34199
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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:

Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding

Deposition date:

2017-11-13

Original release date:

2018-01-12

Authors:

Erat, M.; Besic, E.; Oberhuber, M.; Johannsen, S.; Sigel, R.

Citation:

Citation: Erat, M.; Besic, E.; Oberhuber, M.; Johannsen, S.; Sigel, R.; Erat, M.; Zerbe, O.; Fox, T.; Sigel, R.. "Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding." J. Biol. Inorg. Chem. 23, 167-177 (2018).
PubMed: 29218637

Assembly members:

Assembly members:
entity_1, polymer, 27 residues, 8800.562 Da.

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):
entity_1: GGAGCGGGGGXGXAAACCXA XCGCXCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	203

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 27 residues - 8800.562 Da.

1

G

A

G

C

G

2

U37

G

U37

A

C

U37

A

3

U37

C

G

C

U37

C

Samples:

sample_2: alpha-thio-D6-27 0.7 mM

sample_1: alpha-thio-D6-27 2 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.7 pD; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.7; pressure: 1 atm; temperature: 275 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-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

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

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 600 MHz