8QQ3

Streptavidin with a Ni-cofactor

• PDB DOI: https://doi.org/10.2210/pdb8QQ3/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-03 Released: 2024-02-07 
• Deposition Author(s): Zhang, K., Jakob, R.P., Ward, T.R.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

An artificial nickel chlorinase based on the biotin-streptavidin technology.

Yu, K., Zhang, K., Jakob, R.P., Maier, T., Ward, T.R.

(2024) Chem Commun (Camb) 60: 1944-1947

• PubMed: 38277163 
• DOI: https://doi.org/10.1039/d3cc05847f
• Primary Citation of Related Structures:  
  8QQ3


• PubMed Abstract: 
  

  Herein, we report on an artificial nickel chlorinase (ANCase) resulting from anchoring a biotinylated nickel-based cofactor within streptavidin (Sav). The resulting ANCase was efficient for the chlorination of diverse C(sp ³ )-H bonds. Guided by the X-ray analysis of the ANCase, the activity of the artificial chlorinase could be significantly improved. This approach opens interesting perspectives for late-stage functionalization of organic intermediates as it complements biocatalytic chlorination strategies.

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Organizational Affiliation: 

Department of Chemistry, University of Basel, Mattenstrasse 22, Basel, CH-4058, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69 kDa 
• Atom Count: 4,400 
• Modelled Residue Count: 502 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	159	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WKF (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	4-[4-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butylamino]-~{N}1,~{N}1'-di(quinolin-8-yl)cyclohexane-1,1-dicarboxamide C35 H39 N7 O3 S RCUCAUCKUVJHRT-QYDYLWNGSA-N
NI	F [auth A], H [auth B], J [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.028	α = 90
b = 88.712	β = 97.13
c = 57.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Zhang, K., Jakob, R.P., Ward, T.R.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	NCCR Catalysis (Grant Number 180544), a National Centre of Competence Grant

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Database references