BMRB Entry 4646

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PDB ID: 1fyi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR4646
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structural NMR characterization of an 11-mer DNA Duplex Containing a 2'-deoxyaristeromycin 8-oxo-Guanine pair, nonhydrolyzable substrate analog for the DNA repair enzyme MutY

Deposition date:

2000-09-30

Original release date:

2010-07-16

Authors:

Smirnov, S.; Johnson, F.; De los Santos, C.

Citation:

Citation: Smirnov, S.; Johnson, F.; Marumoto, R.; De los Santos, C.. "Structure of an 11-mer DNA Duplex Containing the Carbocyclic Nucleotide Analog: 2'-deoxyaristeromycin" J. Biomol. Struct. Dyn. 17, 981-991 (2000).
PubMed: 10949165

Assembly members:

Assembly members:
5'-D(*CP*AP*GP*TP*GP*(2AR)P*GP*TP*CP*AP*C)-3', polymer, 11 residues, Formula weight is not available
5'-D(*GP*TP*GP*AP*CP*(8OG)P*CP*AP*CP*TP*G)-3', polymer, 11 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):
5'-D(*CP*AP*GP*TP*GP*(2AR)P*GP*TP*CP*AP*C)-3': CAGTGXGTCAC
5'-D(*GP*TP*GP*AP*CP*(8OG)P*CP*AP*CP*TP*G)-3': GTGACXCACTG

Data sets:

assigned_chemical_shifts
- chemical_shift_set_+strand
- chemical_shift_set_-strand

Data type	Count
1H chemical shifts	144
31P chemical shifts	17

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5'-D(CPAPGPTPGP(2AR)PGPTPCPAP*C)-3'	1
2	5'-D(GPTPGPAPCP(8OG)PCPAPCPTP*G)-3'	2

Entities:

Entity 1, 5'-D(*CP*AP*GP*TP*GP*(2AR)P*GP*TP*CP*AP*C)-3' 11 residues - Formula weight is not available

1

DC

DA

DG

DT

DG

2AR

DG

DT

DC

DA

2

DC

Entity 2, 5'-D(*GP*TP*GP*AP*CP*(8OG)P*CP*AP*CP*TP*G)-3' 11 residues - Formula weight is not available

1

DG

DT

DG

DA

DC

8OG

DC

DA

DC

DT

2

DG

Samples:

sample_1: DNA 280 OD260; phosphate buffer 50 mM; H2O 90%; D2O 10%

sample_2: DNA 280 OD260; phosphate buffer 50 mM; D2O 99.6%

sample_cond_1: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 284 K

sample_cond_2: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	not available
DQF-COSY	not available	not available	not available
TOCSY	not available	not available	not available

Software:

VNMR v5 - collection

FELIX v95 - data analysis

X-PLOR v3.8 - refinement

NMR spectrometers:

Varian UNITYplus 600 MHz