7BSE

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (T5A mutant)

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2020-03-30 Released: 2020-12-16 
  • Deposition Author(s): Kondo, J., Cerretani, C., Vosch, T.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report



Literature

Mutation of position 5 as a crystal engineering tool for a NIR-emitting DNA-stabilized Ag16 nanocluster.

Cerretani, C.Kondo, J.Vosch, T.

(2020) CrystEngComm 22: 8136-8141


Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')A, B, C, D10synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    AG
    Query on AG

    Download Ideal Coordinates CCD File 
    A, B, C, D
    SILVER ION
    Ag
    FOIXSVOLVBLSDH-UHFFFAOYSA-N
     Ligand Interaction
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    B, C
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 Å
    • R-Value Free: 0.137 
    • R-Value Work: 0.124 
    • R-Value Observed: 0.126 
    • Space Group: P 43 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 45.353α = 90
    b = 45.353β = 90
    c = 82.722γ = 90
    Software Package:
    Software NamePurpose
    XSCALEdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    PHENIXphasing
    XDSdata reduction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

    Revision History 

    • Version 1.0: 2020-12-16
      Type: Initial release