6M2P

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (A10-deletion mutant)

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

  • Deposited: 2020-02-28 Released: 2020-07-01 
  • 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: 1.13 Å
  • R-Value Free: 0.096 
  • R-Value Work: 0.085 
  • R-Value Observed: 0.086 

wwPDB Validation 3D Report Full Report



Literature

Removal of the A10 adenosine in a DNA-stabilized Ag16 nanocluster.

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

(2020) RSC Adv 10: 23854-23860


Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')A, B, C, D9synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG
Query on AG

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

Download CCD File 
A, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.096 
  • R-Value Work: 0.085 
  • R-Value Observed: 0.086 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.211α = 90
b = 33.713β = 98.11
c = 58.551γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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: 2020-07-01
    Type: Initial release