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- PDB-6j2w: The structure of OBA3-OTA complex -

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Basic information

Entry
Database: PDB / ID: 6j2w
TitleThe structure of OBA3-OTA complex
ComponentsDNA (5'-D(*CP*GP*GP*GP*GP*CP*GP*AP*AP*GP*CP*GP*GP*GP*TP*CP*CP*CP*G)-3')
KeywordsDNA / triple helix / hairpin
Function / homologyChem-B2U / 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
Ministry of Science and Technology (China)2017YFA0505400 China
National Natural Science Foundation of China21190041 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure-guided post-SELEX optimization of an ochratoxin A aptamer.
Authors: Xu, G. / Zhao, J. / Liu, N. / Yang, M. / Zhao, Q. / Li, C. / Liu, M.
History
DepositionJan 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_nmr_software.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*GP*GP*GP*CP*GP*AP*AP*GP*CP*GP*GP*GP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3172
Polymers5,9131
Non-polymers4041
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR titration demonstrated the complex formation of DNA aptamer with OTA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*CP*GP*GP*GP*GP*CP*GP*AP*AP*GP*CP*GP*GP*GP*TP*CP*CP*CP*G)-3')


Mass: 5912.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-B2U / N-[(3R)-5-chloro-8-hydroxy-3-methyl-1-oxo-3,4-dihydro-1H-2-benzopyran-7-carbonyl]-D-phenylalanine


Mass: 403.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18ClNO6 / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
122isotropic12D NOESY
132isotropic12D DQF-COSY
142isotropic12D TOCSY
151isotropic22D JRHMBC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.8 mM OBA3, 90% H2O/10% D2O1.8 mM nucleic acid in solution containing 10 mM Na2HPO4/KH2PO4 and 10 mM MgCl2NA90% H2O/10% D2O
solution21.8 mM OBA3, 100% D2O1.8 mM nucleic acid in solution containing 10 mM Na2HPO4/KH2PO4 and 10 mM MgCl2NA100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMOBA3natural abundance1
1.8 mMOBA3natural abundance2
Sample conditionsDetails: 1.8 mM nucleic acid in solution containing 10 mM Na2HPO4/KH2PO4 and 10 mM MgCl2
Ionic strength: 10 mM MgCl2 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
X-PLOR2.47Brungerstructure calculation
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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