5CSE | pdb_00005cse

Streptavidin-S112Y-K121E Complexed with Palladium-Containing Biotin Ligand

• PDB DOI: https://doi.org/10.2210/pdb5CSE/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-23 Released: 2015-11-04 
• Deposition Author(s): Finke, A.D., Vera, L., Marsh, M., Chatterjee, A., Ward, T.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

An enantioselective artificial Suzukiase based on the biotin-streptavidin technology.

Chatterjee, A., Mallin, H., Klehr, J., Vallapurackal, J., Finke, A.D., Vera, L., Marsh, M., Ward, T.R.

(2016) Chem Sci 7: 673-677

• PubMed: 29896353 
• DOI: https://doi.org/10.1039/c5sc03116h
• Primary Citation Related Structures: 
  5CSE


• PubMed Abstract: 
  

  Introduction of a biotinylated monophosphine palladium complex within streptavidin affords an enantioselective artificial Suzukiase. Site-directed mutagenesis allowed the optimization of the activity and the enantioselectivity of this artificial metalloenzyme. A variety of atropisomeric biaryls were produced in good yields and up to 90% ee. The hybrid catalyst described herein shows comparable TOF to the previous aqueous-asymmetric Suzuki catalysts, and excellent stability under the reaction conditions to realize higher TON through longer reaction time.

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Organizational Affiliation: 
• Department of Chemistry , University of Basel , Spitalstrasse 51 , 4056 Basel , Switzerland . Email: [e-mail].
Swiss Light Source , Paul Scherrer Institute 5232 Villigen PSI , Switzerland.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.71 kDa 
• Atom Count: 1,973 
• Modeled Residue Count: 243 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	159	Streptomyces avidinii	Mutation(s): 2
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
SVP	C [auth A], E [auth B]	chloro{di-tert-butyl[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]-lambda~5~-phosphanyl}(1-phenylprop-1-ene-1,3-diyl-kappa~2~C~1~,C~3~)palladium C29 H46 Cl N3 O2 P Pd S VFIKYJJBNYQPLX-CRZSKOOBSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.368	α = 90
b = 81.46	β = 90
c = 90.811	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Finke, A.D., Vera, L., Marsh, M., Chatterjee, A., Ward, T.R.

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 2.0: 2018-07-11
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description