BMRB Entry 30546

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30546
MolProbity Validation Chart

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Title:
RNA Duplex containing the internal loop 5'-GCUU/3'-UUCG
Deposition date:
2018-11-29
Original release date:
2019-02-08
Authors:
Berger, K.; Kennedy, S.; Turner, D.
Citation:

Citation: Berger, K.; Kennedy, S.; Turner, D.. "Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures"  Biochemistry 58, 1094-1108 (2019).
PubMed: 30702283

Assembly members:

Assembly members:
RNA (5'-R(*CP*GP*CP*AP*GP*CP*UP*UP*AP*CP*GP*C)-3'), polymer, 12 residues, 3787.312 Da.
RNA (5'-R(*GP*CP*GP*UP*GP*CP*UP*UP*UP*GP*CP*G)-3'), polymer, 12 residues, 3821.280 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 32644   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA (5'-R(*CP*GP*CP*AP*GP*CP*UP*UP*AP*CP*GP*C)-3'): CGCAGCUUACGC
RNA (5'-R(*GP*CP*GP*UP*GP*CP*UP*UP*UP*GP*CP*G)-3'): GCGUGCUUUGCG

Data sets:
Data typeCount
13C chemical shifts24
1H chemical shifts148
31P chemical shifts7

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 12 residues - 3787.312 Da.

1   CGCAGCUUAC
2   GC

Entity 2, entity_2 12 residues - 3821.280 Da.

1   GCGUGCUUUG
2   CG

Samples:

sample_1: RNA (5'-R(*CP*GP*CP*AP*GP*CP*UP*UP*AP*CP*GP*C)-3'), none, 1 mM; RNA (5'-R(*GP*CP*GP*UP*GP*CP*UP*UP*UP*GP*CP*G)-3'), none, 1 mM; sodium chloride 80 mM; sodium phosphate 50 mM

sample_conditions_1: ionic strength: 130 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

SPARKY, Goddard - data analysis

vnmr, Goddard - collection

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

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

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz