6M2P | pdb_00006m2p

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

• PDB DOI: https://doi.org/10.2210/pdb6M2P/pdb
• NAKB: 6M2P

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.096 (Depositor), 0.091 (DCC) 
• R-Value Work: 
  0.085 (Depositor), 0.082 (DCC) 
• R-Value Observed: 
  0.086 (Depositor) 

Starting Model: experimental

Literature

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

Cerretani, C., Kondo, J., Vosch, T.

(2020) RSC Adv 10: 23854-23860

• DOI: https://doi.org/10.1039/D0RA02672G

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.48 kDa 
• Atom Count: 968 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')	A, B, C, D	9	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], MA [auth D], NA [auth D], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N
CA	M [auth A], OA [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	FA [auth C], N [auth A], PA [auth D], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.096 (Depositor), 0.091 (DCC) 
• R-Value Work:  0.085 (Depositor), 0.082 (DCC) 
• R-Value Observed: 0.086 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.211	α = 90
b = 33.713	β = 98.11
c = 58.551	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Kondo, J., Cerretani, C., Vosch, T.

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

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 2.0: 2023-03-22
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Refinement description