BMRB Entry 36411

Name: Aptamer enhancing peroxidase activity of myoglobin
Published: 2021-08-26

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PDB ID: 7e5p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36411
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:

Aptamer enhancing peroxidase activity of myoglobin

Deposition date:

2021-02-19

Original release date:

2021-08-26

Authors:

Tsukakoshi, K.; Matsugami, A.; Khunathai, K.; Kanazashi, M.; Yamagishi, Y.; Nakama, K.; Oshikawa, D.; Hayashi, F.; Kuno, H.; Ikebukuro, K.

Citation:

Citation: Tsukakoshi, Kaori; Yamagishi, Yasuko; Kanazashi, Mana; Nakama, Kenta; Oshikawa, Daiki; Savory, Nasa; Matsugami, Akimasa; Hayashi, Fumiaki; Lee, Jinhee; Saito, Taiki; Sode, Koji; Khunathai, Kanjana; Kuno, Hitoshi; Ikebukuro, Kazunori. "G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol." Nucleic Acids Res. 49, 6069-6081 (2021).
PubMed: 34095949

Assembly members:

Assembly members:
DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), polymer, 16 residues, 5131.298 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 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 (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'): GGGTGGGTTGGGAGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	67
1H chemical shifts	153

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 16 residues - 5131.298 Da.

1

DG

DT

DG

DT

DG

2

DG

DA

DG

Samples:

sample_1: DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') 1 mM; DSS 100 uM; Potassium phosphate buffer pH 6.5 10 mM; D2O, [U-2H], 100%

sample_2: DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') 1 mM; DSS 100 uM; Potassium phosphate buffer pH 6.5 10 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY 500ms	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 50ms	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY 120ms	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
2D 1H-1H NOESY 50ms	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY 250ms	sample_2	isotropic	sample_conditions_1
2D JR-HMBC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1

Software:

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

Sparky v3.114, Goddard - peak picking

TopSpin v3.5, Bruker Biospin - processing

X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Bruker AVANCE III 700 MHz
Bruker AVANCE III 800 MHz