8OZS | pdb_00008ozs

Populus tremula stable protein 1 with N-terminal binding peptide extension with hemin

• PDB DOI: https://doi.org/10.2210/pdb8OZS/pdb

• Classification: PLANT PROTEIN
• Organism(s): Populus tremula
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2024-03-27 
• Deposition Author(s): Sklyar, J., Zeibaq, Y., Bachar, O., Yehezkeli, O., Adir, N.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

A Bioengineered Stable Protein 1-Hemin Complex with Enhanced Peroxidase-Like Catalytic Properties.

Zeibaq, Y., Bachar, O., Sklyar, J., Adir, N., Yehezkeli, O.

(2024) Small Sci 4: 2400025-2400025

• PubMed: 40212758 
• DOI: https://doi.org/10.1002/smsc.202400025
• Primary Citation Related Structures: 
  8OZ4, 8OZO, 8OZS


• PubMed Abstract: 
  

  Enzymes have gained their unique efficiency and catalytic activity through billions of years of evolution, perfecting their active site to a desired reaction. Inspired by nature, a novel enzyme-mimicking platform is designed based on stable protein 1 (SP1) to create a nano-compartment that mimics peroxidase activity. The biohybrid reveals enhanced activity over the hemin cofactor alone and improved stability in organic solvents in comparison to native peroxidase. Furthermore, the utilization of the obtained biohybrid in an optical glucose biosensing platform is shown. The biohybrid crystallographic structure is solved, indicating that the SP1 structure is not affected by the hemin coordination. This work opens the path for developing new cofactor binding centers in engineered protein scaffolds for various artificial catalytic processes.

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Organizational Affiliation: 
• Department of Biotechnology and Food Engineering Technion-Israel Institute of Technology Haifa 3200003 Israel.
Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 320000 Israel.
Russell Berrie Nanotechnology Institute Technion-Israel Institute of Technology Haifa 3200003 Israel.
The Nancy and Stephen Grand Technion Energy Program Technion-Israel Institute of Technology Haifa 3200003 Israel.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 328.35 kDa 
• Atom Count: 22,623 
• Modeled Residue Count: 2,544 
• Deposited Residue Count: 2,880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stable protein 1	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	120	Populus tremula	Mutation(s): 0  Gene Names: sp1
UniProt
Find proteins for Q9AR79 (Populus tremula) Explore Q9AR79  Go to UniProtKB:  Q9AR79

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.059	α = 90
b = 94.372	β = 90.22
c = 168.069	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: 2024-03-27 
Deposition Author(s): Sklyar, J., Zeibaq, Y., Bachar, O., Yehezkeli, O., Adir, N.

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Funding Organization	Location	Grant Number
Other government	Israel	2028751

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Database references, Structure summary