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- PDB-8if5: AFB1-AF26 APTAMER COMPLEX -

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Basic information

Entry
Database: PDB / ID: 8if5
TitleAFB1-AF26 APTAMER COMPLEX
ComponentsAFB1 DNA aptamer (26-MER)
KeywordsDNA / DNA aptamer / Aflatoxin B1 (AFB1) / Stem-loop
Function / homologyAFLATOXIN B1 / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsXu, G.H. / Wang, C. / Li, C.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21925406 China
National Natural Science Foundation of China (NSFC)21874149 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer.
Authors: Xu, G. / Wang, C. / Yu, H. / Li, Y. / Zhao, Q. / Zhou, X. / Li, C. / Liu, M.
History
DepositionFeb 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AFB1 DNA aptamer (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2552
Polymers7,9431
Non-polymers3121
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain AFB1 DNA aptamer (26-MER)


Mass: 7943.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AFT / AFLATOXIN B1


Mass: 312.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
142isotropic12D 1H-1H NOESY
151isotropic12D 31P-1H COSY
163isotropic32D 1H-13C JRHMBC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM AFB1 DNA aptamer (26-MER), 2 mM AFB1, 10 mM D TRIS-D11, 50 mM sodium chloride, 50 mM MgCL2, 100% D2O1 mM AF26 with 2 equivalents of AFB1 in 10 mM Tris-D11, 50 mM NaCl, and 50 mM MgCl2 (pH 7.5)1H100% D2O
solution21 mM AFB1 DNA aptamer (26-MER), 2 mM AFB1, 10 mM D TRIS-D11, 50 mM sodium chloride, 50 mM MgCL2, 90% H2O/10% D2O1 mM AF26 with 2 equivalents of AFB1 in 10 mM Tris-D11, 50 mM NaCl, and 50 mM MgCl2 (pH 7.5)1H90% H2O/10% D2O
solution33 mM AFB1 DNA aptamer (26-MER), 6 mM AFB1, 10 mM D TRIS-D11, 50 mM sodium chloride, 50 mM MgCL2, 90% H2O/10% D2O3 mM AF26 with 2 equivalents of AFB1 in 10 mM Tris-D11, 50 mM NaCl, and 50 mM MgCl2 (pH 7.5)1H90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAFB1 DNA aptamer (26-MER)natural abundance1
2 mMAFB1natural abundance1
10 mMTRIS-D11D1
50 mMsodium chloridenatural abundance1
50 mMMgCL2natural abundance1
1 mMAFB1 DNA aptamer (26-MER)natural abundance2
2 mMAFB1natural abundance2
10 mMTRIS-D11D2
50 mMsodium chloridenatural abundance2
50 mMMgCL2natural abundance2
3 mMAFB1 DNA aptamer (26-MER)natural abundance3
6 mMAFB1natural abundance3
10 mMTRIS-D11D3
50 mMsodium chloridenatural abundance3
50 mMMgCL2natural abundance3
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7.5 / PH err: 0.2 / Pressure: 1 atm / Temperature: 278 K / Temperature err: 1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
Refinement
MethodSoftware ordinal
simulated annealing2
torsion angle dynamics1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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