BMRB Entry 16055

Name: Dimeric solution structure of the cyclic octamer d(pCGCTCCGT)
Published: 2009-04-17

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PDB ID: 2k97
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16055
MolProbity Validation Chart

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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:

Dimeric solution structure of the cyclic octamer d(pCGCTCCGT)

Deposition date:

2008-12-09

Original release date:

2009-04-17

Authors:

Viladoms, Julia; Escaja, Nuria; Frieden, Miriam; Gomez-Pinto, Irene; Pedroso, Enrique; Gonzalez, Carlos

Citation:

Citation: Viladoms, Julia; Escaja, Nuria; Frieden, Miriam; Gomez-Pinto, Irene; Pedroso, Enrique; Gonzalez, Carlos. "Self-association of short DNA loops through minor groove C:G:G:C tetrads" Nucleic Acids Res. 37, 3264-3275 (2009).
PubMed: 19321501

Assembly members:

Assembly members:
DNA_(cyclic_D(P*CP*GP*CP*TP*CP*CP*GP*T)), polymer, 8 residues, 2408.610 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_(cyclic_D(P*CP*GP*CP*TP*CP*CP*GP*T)): CGCTCCGT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	79

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

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

Entities:

Entity 1, DNA (5'-D(P*CP*CP*GP*TP*CP*GP*CP*T)-3')_1 8 residues - 2408.610 Da.

1

DC

DG

DC

DT

DC

DG

DT

Samples:

sample_1: DNA (cyclic D(P*CP*GP*CP*TP*CP*CP*GP*T))0.1 – 4.0 mM; sodium phosphate 25 mM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 308 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

Software:

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

DYANA, Guntert, Braun and Wuthrich - structure solution

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker DMX 600 MHz
Bruker DMX 800 MHz