BMRB Entry 18626

Title:
NMR Structure of the Self-Complementary 10 mer DNA Duplex 5'-GGATATATCC-3' in Complex with Netropsin
Deposition date:
2012-07-31
Original release date:
2013-01-22
Authors:
Rettig, Michael; Germann, Markus; Wilson, W. David; Wang, Shuo
Citation:

Citation: Rettig, Michael; Germann, Markus; Wang, Shuo; Wilson, W. David. "Molecular basis for sequence-dependent induced DNA bending."  Chembiochem 14, 323-331 (2013).
PubMed: 23355266

Assembly members:

Assembly members:
DNA_10_mer, polymer, 10 residues, 3044.042 Da.
NETROPSIN, non-polymer, 430.464 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_10_mer: GGATATATCC

Data sets:
Data typeCount
1H chemical shifts198

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')_11
2DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')_21
3NETROPSIN2

Entities:

Entity 1, DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')_1 10 residues - 3044.042 Da.

1   DGDGDADTDADTDADTDCDC

Entity 2, NETROPSIN - C18 H26 N10 O3 - 430.464 Da.

1   NT

Samples:

sample_1_D2O: DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 0.9 mM; NETROPSIN 0.9 mM; D2O 100%

sample_1_H2O: DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 0.9 mM; NETROPSIN 0.9 mM; D2O 10%; H2O 90%

sample_1_Pf1: DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 0.6 mM; Pf1 phage 9 mg/mL; NETROPSIN 0.6 mM; D2O 100%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1_D2Oisotropicsample_conditions_1
2D 1H-1H NOESYsample_1_H2Oisotropicsample_conditions_1
2D DQF-COSYsample_1_D2Oisotropicsample_conditions_1
2D 1H-1H NOESYsample_1_Pf1anisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1_Pf1anisotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1_Pf1anisotropicsample_conditions_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz