BMRB Entry 18626

Name: NMR Structure of the Self-Complementary 10 mer DNA Duplex 5&#039;-GGATATATCC-3&#039; in Complex with Netropsin
Published: 2013-01-22

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PDB ID: 2lwh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18626
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	198

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')_1	1
2	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')_2	1
3	NETROPSIN	2

Entities:

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

1

DG

DA

DT

DA

DT

DA

DT

DC

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1_H2O	isotropic	sample_conditions_1
2D DQF-COSY	sample_1_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1_Pf1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1_Pf1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1_Pf1	anisotropic	sample_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