BMRB Entry 11438

Name: DNA oligomer containing ethylene cross-linked cyclic 2&#039;-deoxyuridylate dimer
Published: 2011-06-22

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PDB ID: 2rrr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11438
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:

DNA oligomer containing ethylene cross-linked cyclic 2'-deoxyuridylate dimer

Deposition date:

2011-03-24

Original release date:

2011-06-22

Authors:

Furuita, Kyoko; Murata, Shunpei; Jee, JunGoo; Ichikawa, Satoshi; Matsuda, Akira; Kojima, Chojiro

Citation:

Citation: Furuita, Kyoko; Murata, Shunpei; Jee, JunGoo; Ichikawa, Satoshi; Matsuda, Akira; Kojima, Chojiro. "Structural Feature of Bent DNA Recognized by HMGB1" J. Am. Chem. Soc. 133, 5788-5790 (2011).
PubMed: 21443191

Assembly members:

Assembly members:
Ethylene-DNA, polymer, 28 residues, 111.103 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):
Ethylene-DNA: CCTTCATTACATCCGGATGT AATGAAGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	211

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ethylene-DNA	1

Entities:

Entity 1, Ethylene-DNA 28 residues - 111.103 Da.

1

DC

DT

DC

DA

DT

DA

DC

2

DA

DT

DC

DG

DA

DT

DG

DT

3

DA

DT

DG

DA

DG

Samples:

sample_1: Ethylene-DNA 0.7 mM; sodium phosphate 50 mM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_2: Ethylene-DNA 0.7 mM; sodium phosphate 50 mM; sodium chloride 100 mM; D2O 100%

sample_conditions_1: pH: 6.8; temperature: 283 K

sample_conditions_2: pH: 6.8; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_2
2D DQF-COSY	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

MARDIGRAS, Brandan, A. Borgias, Paul D. Thomas, He Liu and Anil Kumar - structure solution

NMR spectrometers:

Bruker Avance 500 MHz
Bruker DRX 800 MHz