BMRB Entry 52690

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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/BMR52690
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
RKEC1-dopamine 298K
Deposition date:
2024-11-11
Original release date:
2025-12-03
Authors:
Kaiyum, Yunus; Largy, Eric; Chao, Emily; Vialet, Brune; Johnson, Philip; Mackereth, Cameron
Citation:

Citation: Kaiyum, Yunus; Largy, Eric; Chao, Emily; Minh-Dat, Nguyen; Vialet, Brune; Dauphin-Ducharme, Philippe; Johnson, Philip; Mackereth, Cameron. "Dopamine binding by a DNA aptamer devoid of canonical duplex or G-quadruplex"  .

Assembly members:

Assembly members:
entity_1, polymer, 27 residues, Formula weight is not available
entity_LDP, non-polymer, 153.178 Da.

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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TTGAAGGTTCGTTCGCAGGT GTGGAGT

Data sets:
Data typeCount
13C chemical shifts145
15N chemical shifts8
1H chemical shifts261

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA aptamer1
2dopamine2

Entities:

Entity 1, DNA aptamer 27 residues - Formula weight is not available

1   DTDTDGDADADGDGDTDTDC
2   DGDTDTDCDGDCDADGDGDT
3   DGDTDGDGDADGDT

Entity 2, dopamine - C8 H11 N O2 - 153.178 Da.

1   LDP

Samples:

sample_1: RKEC1 2 mM; dopamine 2.5 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_2: RKEC1 2 mM; dopamine 2.25 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_3: RKEC1 1.5 mM; dopamine 1.75 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_4: RKEC1 1.5 mM; dopamine 1.75 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_5: RKEC1 1.5 mM; dopamine 1.75 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_6: RKEC1 1.5 mM; dopamine 1.75 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_7: RKEC1 1.5 mM; dopamine 1.75 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_8: RKEC1 1.5 mM; dopamine 1.75 mM; sodium phosphate 20 mM; sodium chloride 140 mM; magnesium chloride 2 mM

sample_conditions_1: ionic strength: 170 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
1D 1Hsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-15N HSQCsample_6isotropicsample_conditions_1
2D 1H-15N HSQCsample_6isotropicsample_conditions_1
2D 1H-13C HSQCsample_6isotropicsample_conditions_1
2D 1H-15N HSQCsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_7isotropicsample_conditions_1
2D 1H-13C HSQCsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_8isotropicsample_conditions_1
2D 1H-13C HSQCsample_8isotropicsample_conditions_1
2D DQF-COSYsample_8isotropicsample_conditions_1

Software:

TOPSPIN v4.1 - collection

NMRPipe - processing

NMRFAM-SPARKY v1.470 - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker AVANCE NEO 700 MHz
  • Bruker AVANCE NEO 800 MHz