BMRB Entry 34296

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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/BMR34296
MolProbity Validation Chart

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Title:
Polyamide - DNA complex NMR structure
Deposition date:
2018-07-03
Original release date:
2018-11-21
Authors:
Aman, K.
Citation:

Citation: Aman, Khalid; Padroni, Giacomo; Parkinson, John; Welte, Thomas; Burley, Glenn. "Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues."  Chemistry 25, 2757-2763 (2019).
PubMed: 30407668

Assembly members:

Assembly members:
entity_1, polymer, 13 residues, 3940.603 Da.
entity_FGW, non-polymer, 1250.372 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 32630   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: XCGATGTACATCG

Data sets:
Data typeCount
1H chemical shifts250

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_22

Entities:

Entity 1, entity_1, 1 13 residues - 3940.603 Da.

1   PA9DCDGDADTDGDTDADCDA
2   DTDCDG

Entity 2, entity_2 - C60 H75 N21 O10 - 1250.372 Da.

1   FGW

Samples:

sample_1: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') 1.26 mM; polyamide (PA9) 0.24 mM

sample_2: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') 1.26 mM; polyamide (PA9) 0.24 mM

sample_conditions_1: pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AvanceII 600.13 MHz