7BSE | pdb_00007bse

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

• PDB DOI: https://doi.org/10.2210/pdb7BSE/pdb
• NAKB: 7BSE

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

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

• DOI: https://doi.org/10.1039/D0CE01225D

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.3 kDa 
• Atom Count: 943 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')	A, B, C, D	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	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], L [auth A], M [auth A], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N
CA	AA [auth B], KA [auth C], LA [auth C], MA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.353	α = 90
b = 45.353	β = 90
c = 82.722	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
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: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description