BMRB

Biological Magnetic Resonance Data Bank


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BMRB Entry 25427

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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/BMR25427
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Title: DNA/RNA (28-MER)

Deposition date: 2015-01-14 Original release date: 2015-12-07

Authors: Schmidtke, Sina; Duchardt-Ferner, Elke; Ohlenschlaeger, Oliver; Gottstein, Daniel; Wohnert, Jens

Citation: Schmidtke, Sina; Duchardt-Ferner, Elke; Ohlenschlaeger, Oliver; Gottstein, Daniel; Wohnert, Jens. "What a difference an OH makes: conformational dynamics as the basis for ligand specificity of the neomycin sensing riboswitch"  Angew. Chem. Int. Ed. Engl. ., .-..

Assembly members:
RNA_(27-MER), polymer, 27 residues, 3295.044 Da.
PAROMOMYCIN, non-polymer, 615.628 Da.

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

Experimental source:   Production method: obtained from a collaborator   Host organism: in vitro transcription

Entity Sequences (FASTA):
RNA_(27-MER): GGCUGCUUGUCCUUUAAUGG UCCAGUC

Data typeCount
13C chemical shifts444
15N chemical shifts20
1H chemical shifts622

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA/RNA (28-MER)1
2PAROMOMYCIN2

Entities:

Entity 1, DNA/RNA (28-MER) 27 residues - 3295.044 Da.

1   GGCUGCUUGU
2   CCUUUAAUGG
3   UCCAGUC

Entity 2, PAROMOMYCIN - C23 H45 N5 O14 - 615.628 Da.

1   PAR

Samples:

sample_1: RNA (27-MER) 0.64 mM; Paromomycin 0.64 mM; D2O 10%; H2O 90%

sample_2: RNA (27-MER), 13C; 15N, 0.89 mM; Paromomycin 0.89 mM; D2O 10%; H2O 90%

sample_3: RNA (27-MER), 13C; 15N, 0.89 mM; Paromomycin 0.89 mM; D2O 100%

sample_4: RNA (27-MER), G-]13C; 15N], 0.62 mM; Paromomycin 0.62 mM; D2O 100%

sample_conditions_1: pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_2: pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HNCOsample_2isotropicsample_conditions_1
2D 1H-15N H56C56C4N3Hsample_2isotropicsample_conditions_1
2D 1H-15N HSQC NH2 onlysample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_2
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_2
2D 1H-13C HSQC aliphaticsample_4isotropicsample_conditions_2
3D 1H-13C NOESY-HSQC aliphaticsample_3isotropicsample_conditions_2
3D 1H-13C NOESY-HMQC aromaticsample_3isotropicsample_conditions_2
3D HCCH-COSYsample_3isotropicsample_conditions_2
3D HCCH-TOCSYsample_3isotropicsample_conditions_2
2D 1H-15N lrHSQCsample_3isotropicsample_conditions_2
2D DQF-COSYsample_3isotropicsample_conditions_2
2D 1H-31P HCPsample_3isotropicsample_conditions_2
3D HCCH-TOCSY-E.COSYsample_3isotropicsample_conditions_2
2D 13C filter NOESYsample_3isotropicsample_conditions_2
2D 13C filter TOCSYsample_3isotropicsample_conditions_2
2D quant 31P coupled 1H, 13C HSQCsample_3isotropicsample_conditions_2
2D quant 31P coupled 1H-13C HMQCsample_3isotropicsample_conditions_2

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, peak integration, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker DRX 600 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 950 MHz