BMRB Entry 30485

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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/BMR30485
MolProbity Validation Chart

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Title:
NMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGG)
Deposition date:
2018-06-29
Original release date:
2019-06-26
Authors:
Davis, E.; Hennig, M.; Arya, D.
Citation:

Citation: Davis, E.; Hennig, M.; Arya, D.. "An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences"  .

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 2852.858 Da.
entity_2, polymer, 9 residues, 2621.728 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TGGGCGGGG
entity_2: CCCCGCCCA

Data sets:
Data typeCount
1H chemical shifts133

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 9 residues - 2852.858 Da.

1   DTDGDGDGDCDGDGDGDG

Entity 2, entity_2 9 residues - 2621.728 Da.

1   DCDCDCDCDGDCDCDCDA

Samples:

sample_1: DNA 1.0 mM; DNA 1.0 mM; sodium chloride 25 mM; Na Phosphate 5 mM; EDTA 0.5 mM

sample_2: DNA 900 uM; DNA 900 uM; sodium chloride 25 mM; Na Phosphate 5 mM; EDTA 0.5 mM

sample_conditions_1: ionic strength: 30 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D ECOSYsample_1isotropicsample_conditions_1

Software:

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

AMBER v14.0, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

SPARKY, Goddard - chemical shift assignment

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

3DNA, Lu - data analysis

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker AvanceIII 850 MHz