9XRW | pdb_00009xrw

Probing Positions 3 and 8: Insights into a 960 nm emissive DNA-Stabilized Silver Nanocluster

• PDB DOI: https://doi.org/10.2210/pdb9XRW/pdb
• NAKB: 9XRW

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


• Deposited: 2025-11-20 Released: 2026-01-28 
• Deposition Author(s): Romolini, G., Kanazawa, H., Cerretani, C., Huang, Z., Kondo, J., Vosch, T.
• Funding Organization(s): Independent Research Fund Denmark - Medical Sciences, Novo Nordisk Foundation, European Union (EU), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.156 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Insights into the crystal packing interactions of a 960-nm-emissive DNA-stabilized silver nanocluster.

Romolini, G., Kanazawa, H., Lind, S.W., Cerretani, C., Mollerup, C.B., Liccardo, L., Huang, Z., Lo Leggio, L., Ruck, V., Kondo, J., Vosch, T.

(2026) Chem Commun (Camb) 

• PubMed: 41532973 
• DOI: https://doi.org/10.1039/d5cc06634d
• Primary Citation of Related Structures:  
  9XRW


• PubMed Abstract: 
  

  DNA-stabilized silver nanoclusters (DNA-AgNCs) can be finely tuned through DNA sequence design. Here, we present mutations in a DNA strand that stabilize an [Ag ₂₈ Cl ₂ ] ¹⁴⁺ cluster, which remains largely unaltered, as confirmed by spectroscopy and mass spectrometry. The crystal structure of one mutant further reveals previously unseen packing interactions among DNA-AgNCs.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark. [e-mail].
Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan. [e-mail].
Department of Forensic Medicine, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Biological assembly 8 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 103.86 kDa 
• Atom Count: 5,711 
• Modeled Residue Count: 256 
• Deposited Residue Count: 256 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*CP*GP*CP*GP*TP*GP*CP*CP*GP*CP*GP*AP*A)-3')	A, B, C [auth D], D [auth E], E [auth G], F [auth H], G [auth J], H [auth K], I [auth M], J [auth N], K [auth P], L [auth Q], M [auth S], N [auth T], O [auth V], P [auth W]	16	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	AA [auth A], AB [auth D], AD [auth H], AE [auth K], AF [auth M], AG [auth P], AH [auth S], AI [auth T], AJ [auth W], BA [auth A], BB [auth D], BD [auth H], BE [auth K], BF [auth M], BG [auth P], BH [auth S], BI [auth T], BJ [auth W], CA [auth A], CB [auth D], CC [auth G], CD [auth H], CE [auth K], CG [auth P], CH [auth S], CI [auth T], CJ [auth W], DA [auth A], DB [auth D], DC [auth G], DD [auth H], DE [auth K], DG [auth P], DH [auth S], DI [auth V], DJ [auth W], EB [auth D], EC [auth G], ED [auth H], EE [auth K], EG [auth P], EH [auth S], EI [auth V], EJ [auth W], FB [auth D], FC [auth G], FD [auth H], FE [auth K], FF [auth N], FG [auth P], FH [auth S], FI [auth V], FJ [auth W], GA [auth B], GB [auth D], GC [auth G], GD [auth H], GE [auth K], GF [auth N], GG [auth P], GH [auth S], GI [auth V], GJ [auth W], HA [auth B], HB [auth D], HC [auth G], HE [auth K], HF [auth N], HH [auth S], HI [auth V], IA [auth B], IB [auth D], IC [auth G], ID [auth J], IE [auth K], IF [auth N], IH [auth S], II [auth V], JA [auth B], JB [auth D], JC [auth G], JD [auth J], JE [auth K], JF [auth N], JH [auth S], JI [auth V], KA [auth B], KC [auth G], KD [auth J], KE [auth K], KF [auth N], KG [auth Q], KH [auth S], KI [auth V], LA [auth B], LC [auth G], LD [auth J], LE [auth K], LF [auth N], LG [auth Q], LH [auth S], LI [auth V], MA [auth B], MB [auth E], MC [auth G], MD [auth J], MF [auth N], MG [auth Q], MH [auth S], MI [auth V], NA [auth B], NB [auth E], NC [auth G], ND [auth J], NF [auth N], NG [auth Q], NI [auth V], OA [auth B], OB [auth E], OC [auth G], OD [auth J], OE [auth M], OF [auth N], OG [auth Q], OI [auth V], PA [auth B], PB [auth E], PC [auth G], PD [auth J], PE [auth M], PF [auth N], PG [auth Q], PH [auth T], PI [auth V], Q [auth A], QA [auth B], QB [auth E], QD [auth J], QE [auth M], QF [auth N], QG [auth Q], QH [auth T], QI [auth V], R [auth A], RA [auth B], RB [auth E], RD [auth J], RE [auth M], RF [auth N], RG [auth Q], RH [auth T], S [auth A], SA [auth B], SB [auth E], SD [auth J], SE [auth M], SF [auth N], SG [auth Q], SH [auth T], T [auth A], TA [auth B], TB [auth E], TC [auth H], TD [auth J], TE [auth M], TF [auth P], TG [auth Q], TH [auth T], TI [auth W], U [auth A], UB [auth E], UC [auth H], UD [auth J], UE [auth M], UF [auth P], UG [auth Q], UH [auth T], UI [auth W], V [auth A], VB [auth E], VC [auth H], VD [auth J], VE [auth M], VF [auth P], VG [auth Q], VH [auth T], VI [auth W], W [auth A], WA [auth D], WB [auth E], WC [auth H], WE [auth M], WF [auth P], WG [auth Q], WH [auth T], WI [auth W], X [auth A], XA [auth D], XB [auth E], XC [auth H], XE [auth M], XF [auth P], XG [auth Q], XH [auth T], XI [auth W], Y [auth A], YA [auth D], YB [auth E], YC [auth H], YD [auth K], YE [auth M], YF [auth P], YH [auth T], YI [auth W], Z [auth A], ZA [auth D], ZB [auth E], ZC [auth H], ZD [auth K], ZE [auth M], ZF [auth P], ZG [auth S], ZH [auth T], ZI [auth W]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N
SR	BC [auth E], EF [auth M], FA [auth A], HD [auth H], JG [auth P], LB [auth D], NE [auth K], SC [auth G], VA [auth B], XD [auth J], YG [auth Q]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	AC [auth E], CF [auth M], DF [auth M], EA [auth A], HG [auth P], IG [auth P], KB [auth D], ME [auth K], NH [auth S], OH [auth S], QC [auth G], RC [auth G], RI [auth V], SI [auth V], UA [auth B], WD [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.156 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.555	α = 90
b = 108.107	β = 90.03
c = 108.199	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
Sir2014	phasing
AutoSol	phasing
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Romolini, G., Kanazawa, H., Cerretani, C., Huang, Z., Kondo, J., Vosch, T.

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Funding Organization	Location	Grant Number
Independent Research Fund Denmark - Medical Sciences	Denmark	0136-00024B
Novo Nordisk Foundation	Denmark	NNF22OC0073734
European Union (EU)	European Union	101151897
Independent Research Fund Denmark - Medical Sciences	Denmark	3103-00279B
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121014

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release