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- PDB-7w9n: THE STRUCTURE OF OBA33-OTA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 7w9n
TitleTHE STRUCTURE OF OBA33-OTA COMPLEX
ComponentsOTA DNA APTAMER (33-MER)
KeywordsDNA / duplex / G-quadruplex
Function / homologyChem-97U / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsXu, G.H. / Li, C.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21874149 China
National Natural Science Foundation of China (NSFC)21190041 China
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer.
Authors: Xu, G. / Zhao, J. / Yu, H. / Wang, C. / Huang, Y. / Zhao, Q. / Zhou, X. / Li, C. / Liu, M.
History
DepositionDec 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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: OTA DNA APTAMER (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7762
Polymers10,3731
Non-polymers4041
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain OTA DNA APTAMER (33-MER)


Mass: 10372.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-97U / (2~{S})-2-[[(3~{R})-5-chloranyl-3-methyl-8-oxidanyl-1-oxidanylidene-3,4-dihydroisochromen-7-yl]carbonylamino]-3-phenyl-propanoic acid


Mass: 403.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18ClNO6 / 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 1H-1H DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic22D 1H-31P COSY
252isotropic12D 1H-1H NOESY
172isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM OBA33, 10 mM Na2HPO4/KH2PO4, 120 mM NaCl, 5 mM KCl, 10 mM MgCl2, 100% D2Onatural abundance100% D2O
solution21.0 mM OBA33, 10 mM Na2HPO4/KH2PO4, 120 mM NaCl, 5 mM KCl, 10 mM MgCl2, 90% H2O/10% D2Onatural abundance90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMOBA33natural abundance1
10 mMNa2HPO4/KH2PO4natural abundance1
120 mMNaClnatural abundance1
5 mMKClnatural abundance1
10 mMMgCl2natural abundance1
1.0 mMOBA33natural abundance2
10 mMNa2HPO4/KH2PO4natural abundance2
120 mMNaClnatural abundance2
5 mMKClnatural abundance2
10 mMMgCl2natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1120 mMconditions_17.4 1 atm308 K
2120 mMconditions_27.4 1 atm288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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