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- PDB-9ktj: Solution NMR structures of ATP-binding DNA aptamer in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 9ktj
TitleSolution NMR structures of ATP-binding DNA aptamer in complex with ATP
ComponentsDNA (34-MER)
KeywordsDNA / DNA aptamer / ATP / three-way junction
Function / homologyADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / energy minimization
AuthorsJiang, Y. / Wan, L. / Guo, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Solution NMR structures of ATP-binding DNA aptamer in complex with ATP
Authors: Jiang, Y. / Guo, P. / Wan, L.
History
DepositionDec 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0962
Polymers10,5891
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 DNA (34-MER)


Mass: 10588.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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 NOESY
142isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS, 99.96%D2O199.96%D2O
solution20.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS, 90% H2O/10% D2O290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDNAnatural abundance1
0.8 mMATPnatural abundance1
10 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
10 mMmagnesium chloridenatural abundance1
0.02 mMDSSnatural abundance1
0.8 mMDNAnatural abundance2
0.8 mMATPnatural abundance2
10 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
10 mMmagnesium chloridenatural abundance2
0.02 mMDSSnatural abundance2
Sample conditionsIonic strength: 70 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
GROMACSGROMACS development teamstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing2
energy minimization3
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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