BMRB Entry 27933

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27933

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Title:
1H, 13C, and 15N chemical shift assignments for loop A of the hairpin ribozyme
Deposition date:
2019-05-31
Original release date:
2026-01-13
Authors:
Fidis, Robert; Ochieng, Patrick; White, Neil; Hoogstraten, Charles
Citation:

Citation: Fidis, Robert; Ochieng, Patrick; White, Neil; Hoogstraten, Charles. "Assigned 1H, 13C, and 15N chemical shifts for Loop A of the Hairpin Ribozyme"  Biomol. NMR Assignments ., .-..

Assembly members:

Assembly members:
Ribozyme, polymer, 30 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: In vitro transcription

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ribozyme: GCGUGCAGUCCUCGAAAGAG AGAAGCAUGC

Data sets:
Data typeCount
13C chemical shifts144
15N chemical shifts20
1H chemical shifts155

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Loop A1

Entities:

Entity 1, Loop A 30 residues - Formula weight is not available

The numbering system is designed to align with the conventional notation for the hairpin ribozyme, in which the substrate strand is denoted -N and +N for residues 5' and 3' of the cleavage site, respectively, and the substrate recognition strand is denoted with unsigned integers.

1   GCGUGCAGUC
2   CUCGAAAGAG
3   AGAAGCAUGC

Samples:

Loop_A_Adn: Ribozyme, [U-13C; U-15N]-Ade, 0.47 mM; DSS 0.1 mM; sodium azide 0.1%; EDTA 20 uM; monosodium phosphate 10 mM

Loop_A_Gua: Ribozyme, [U-13C; U-15N]-Gua, 0.33 mM; DSS 0.1 mM; sodium azide 0.1%; EDTA 20 uM; monosodium phosphate 10 mM

Loop_A_Cyt: Ribozyme, [U-13C; U-15N]-Cyt, 0.39 mM; DSS 0.1 mM; sodium azide 0.1%; EDTA 20 uM; monosodium phosphate 10 mM

Loop_A_Ura: Ribozyme, [U-13C; U-15N]-Ura, 0.46 mM; DSS 0.1 mM; sodium azide 0.1%; EDTA 20 uM; monosodium phosphate 10 mM

N-labeled_Ribozyme: Ribozyme, [U-15N], 1.0 mM; DSS 0.1 mM; sodium azide 0.1%; EDTA 20 uM; monosodium phosphate 10 mM

Unlabeled_Ribozyme: Ribozyme 1.0 mM; DSS 0.1 mM; sodium azide 0.1%; EDTA 20 uM; monosodium phosphate 10 mM

Unlabeled_sample_conditions: pH: 5.5; pressure: 1 atm; temperature: 288 K

N-labeled_sample_cond: pH: 5.5; pressure: 1 atm; temperature: 288 K

Nucleotide_labeled_cond: pH: 5.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQC aromaticLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-13C HSQC riboseLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-1H COSYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-13C COSYLoop_A_AdnisotropicNucleotide_labeled_cond
3D HCCH-COSYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-1H TOCSYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-13C TOCSYLoop_A_AdnisotropicNucleotide_labeled_cond
3D HCCH-TOCSYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-1H NOESYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-13C NOESYLoop_A_AdnisotropicNucleotide_labeled_cond
3D 1H-13C HSQC-NOESYLoop_A_AdnisotropicNucleotide_labeled_cond
3D HCN aromaticLoop_A_AdnisotropicNucleotide_labeled_cond
3D HCN riboseLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-1H E/E NOESYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-1H F/E NOESYLoop_A_AdnisotropicNucleotide_labeled_cond
2D 1H-13C HSQC aromaticLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-13C HSQC riboseLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-1H COSYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-13C COSYLoop_A_GuaisotropicNucleotide_labeled_cond
3D HCCH-COSYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-1H TOCSYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-13C TOCSYLoop_A_GuaisotropicNucleotide_labeled_cond
3D HCCH-TOCSYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-1H NOESYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-13C NOESYLoop_A_GuaisotropicNucleotide_labeled_cond
3D 1H-13C HSQC-NOESYLoop_A_GuaisotropicNucleotide_labeled_cond
3D HCN aromaticLoop_A_GuaisotropicNucleotide_labeled_cond
3D HCN riboseLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-1H E/E NOESYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-1H F/E NOESYLoop_A_GuaisotropicNucleotide_labeled_cond
2D 1H-13C HSQC aromaticLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-13C HSQC riboseLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-1H COSYLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-13C COSYLoop_A_CytisotropicNucleotide_labeled_cond
3D HCCH-COSYLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-1H TOCSYLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-13C TOCSYLoop_A_CytisotropicNucleotide_labeled_cond
3D HCCH-TOCSYLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-1H NOESYLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-13C NOESYLoop_A_CytisotropicNucleotide_labeled_cond
3D 1H-13C HSQC-NOESYLoop_A_CytisotropicNucleotide_labeled_cond
3D HCN aromaticLoop_A_CytisotropicNucleotide_labeled_cond
3D HCN riboseLoop_A_CytisotropicNucleotide_labeled_cond
2D 1H-13C HSQC aromaticLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-13C HSQC riboseLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-1H COSYLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-13C COSYLoop_A_UraisotropicNucleotide_labeled_cond
3D HCCH-COSYLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-1H TOCSYLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-13C TOCSYLoop_A_UraisotropicNucleotide_labeled_cond
3D HCCH-TOCSYLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-1H NOESYLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-13C NOESYLoop_A_UraisotropicNucleotide_labeled_cond
3D 1H-13C HSQC-NOESYLoop_A_UraisotropicNucleotide_labeled_cond
3D HCN aromaticLoop_A_UraisotropicNucleotide_labeled_cond
3D HCN riboseLoop_A_UraisotropicNucleotide_labeled_cond
2D 1H-1H NOESYN-labeled_RibozymeisotropicN-labeled_sample_cond
2D 1H-15N HSQCN-labeled_RibozymeisotropicN-labeled_sample_cond
2D 1H-13C HSQC aliphaticUnlabeled_RibozymeisotropicUnlabeled_sample_conditions
2D 1H-13C HSQC aromaticUnlabeled_RibozymeisotropicUnlabeled_sample_conditions
3D HCCH-COSYUnlabeled_RibozymeisotropicUnlabeled_sample_conditions
3D HCCH-TOCSYUnlabeled_RibozymeisotropicUnlabeled_sample_conditions
3D 1H-13C NOESYUnlabeled_RibozymeisotropicUnlabeled_sample_conditions

Software:

SPARKY, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 900 MHz