6JR4 | pdb_00006jr4

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster

PDB DOI: https://doi.org/10.2210/pdb6JR4/pdb
NAKB: 6JR4

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

Deposited: 2019-04-02 Released: 2019-08-28
Deposition Author(s): Kondo, J., Cerretani, C., Kanazawa, H., Vosch, T.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.146 (Depositor), 0.144 (DCC)
R-Value Work:
0.126 (Depositor), 0.122 (DCC)
R-Value Observed:
0.128 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a NIR-Emitting DNA-Stabilized Ag16Nanocluster.

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

(2019) Angew Chem Int Ed Engl 58: 17153-17157

PubMed: 31411360 Search on PubMed
DOI: https://doi.org/10.1002/anie.201906766
Primary Citation Related Structures:
6JR4

PubMed Abstract:
DNA has been used as a scaffold to stabilize small, atomically monodisperse silver nanoclusters, which have attracted attention due to their intriguing photophysical properties. Herein, we describe the X-ray crystal structure of a DNA-encapsulated, near-infrared emitting Ag ₁₆ nanocluster (DNA-Ag ₁₆ NC). The asymmetric unit of the crystal contains two DNA-Ag ₁₆ NCs and the crystal packing between the DNA-Ag ₁₆ NCs is promoted by several interactions, such as two silver-mediated base pairs between 3'-terminal adenines, two phosphate-Ca ²⁺ -phosphate interactions, and π-stacking between two neighboring thymines. Each Ag ₁₆ NC is confined by two DNA decamers that take on a horse-shoe-like conformation and is almost fully shielded from the solvent environment. This structural insight will aid in the determination of the structure/photophysical property relationship for this class of emitters and opens up new research opportunities in fluorescence imaging and sensing using noble-metal clusters.

Organizational Affiliation

Department of Chemistry and NanoScience Center, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 16.24 kDa
Atom Count: 900
Modeled Residue Count: 40
Deposited Residue Count: 40
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(CPAPCPCPTPAPGPCPGPA)-3')	A, B, C, D	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG (Subject of Investigation/LOI) Query on AG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain FA [auth C] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain E [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], Y [auth C], Z [auth C]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain RA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain RA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain RA [auth D]	RA [auth D], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain RA [auth D] Focus chain X [auth B] Interactions & Density Focus chain RA [auth D] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.146 (Depositor), 0.144 (DCC)
R-Value Work: 0.126 (Depositor), 0.122 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.241	α = 90
b = 33.849	β = 97.81
c = 58.863	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	17H03033

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2019-11-27
Changes: Database references
Version 1.2: 2020-03-25
Changes: Data collection
Version 1.3: 2024-03-27
Changes: Data collection, Database references, Derived calculations