BMRB Entry 17422

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PDB ID: 2l8p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17422
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir

Deposition date:

2011-01-22

Original release date:

2011-02-09

Authors:

Julien, Olivier; Beadle, James; Magee, Wendy; Chatterjee, Subhrangsu; Hostetler, Karl; Evans, David; Sykes, Brian

Citation:

Citation: Julien, Olivier; Beadle, James; Magee, Wendy; Chatterjee, Subhrangsu; Hostetler, Karl; Evans, David; Sykes, Brian. "Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir." J. Am. Chem. Soc. 133, 2264-2274 (2011).
PubMed: 21280608

Assembly members:

Assembly members:
Cidofovir_DNA_duplex_chain_A, polymer, 12 residues, Formula weight is not available
Cidofovir_DNA_duplex_chain_B, polymer, 12 residues, Formula weight is not available

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):
Cidofovir_DNA_duplex_chain_A: CGCATGXTACGC
Cidofovir_DNA_duplex_chain_B: GCGTAGCATGCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	4
1H chemical shifts	162

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Cidofovir DNA duplex, chain A	1
2	Cidofovir DNA duplex, chain B	2

Entities:

Entity 1, Cidofovir DNA duplex, chain A 12 residues - Formula weight is not available

1

DC

DG

DC

DA

DT

DG

L8P

DT

DA

DC

2

DG

DC

Entity 2, Cidofovir DNA duplex, chain B 12 residues - Formula weight is not available

1

DG

DC

DG

DT

DA

DG

DC

DA

DT

DG

2

DC

DG

Samples:

sample_1: Cidofovir DNA duplex, chain_A 2 mM; Cidofovir DNA duplex, chain_B 2 mM; NaCl 50 mM; Na2HPO4 20 mM; EDTA 1 mM; DSS-d6 0.25 mM

sample_conditions_1: ionic strength: 70 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

VNMRJ v2.1B, Varian - collection

NMRPipe v4.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.0.b30, Johnson, One Moon Scientific - chemical shift assignment

MARDIGRAS, T.L. James - NOE calibration

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution

CORMA, T.L. James - structure validation

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz