BMRB Entry 19784

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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/BMR19784
MolProbity Validation Chart

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Title:
Solution structure of the G-triplex truncated-TBA
Deposition date:
2014-02-10
Original release date:
2014-11-17
Authors:
Cerofolini, Linda; Fragai, Marco; Giachetti, Andrea; Limongelli, Vittorio; Luchinat, Claudio; Novellino, Ettore; Parrinello, Michele; Randazzo, Antonio
Citation:

Citation: Cerofolini, Linda; Fragai, Marco; Giachetti, Andrea; Limongelli, Vittorio; Luchinat, Claudio; Novellino, Ettore; Parrinello, Michele; Randazzo, Antonio. "G-triplex structure and formation propensity"  Nucleic Acids Res. ., .-. (2014).
PubMed: 25378342

Assembly members:

Assembly members:
DNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3'), polymer, 11 residues, 3476.284 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):
DNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3'): GGTTGGTGTGG

Data sets:
Data typeCount
13C chemical shifts66
1H chemical shifts119
31P chemical shifts9

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')1

Entities:

Entity 1, DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3') 11 residues - 3476.284 Da.

1   DGDGDTDTDGDGDTDGDTDG
2   DG

Samples:

sample_1: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3') 0.7 mM; potassium chloride 70 mM; potassium phosphate 10 mM; EDTA 0.2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.08 M; pH: 7; pressure: 1 atm; temperature: 274 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H ROESYsample_1isotropicsample_conditions_1
2D JR-HMBCsample_1isotropicsample_conditions_1
E.COSYsample_1isotropicsample_conditions_1
2D 31P-1H HSQCsample_1isotropicsample_conditions_1
2D 31P-1H COSYsample_1isotropicsample_conditions_1
2D 13C-1H HSQCsample_1isotropicsample_conditions_1
IPAPsample_1isotropicsample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

CARA v2.1, Keller and Wuthrich - chemical shift assignment

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz
  • Bruker DRX 500 MHz
  • Bruker Avance 950 MHz