8OZS | pdb_00008ozs

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1002/smsc.202400025
  • Primary Citation of 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.


  • Organizational Affiliation
    • Department of Biotechnology and Food Engineering Technion-Israel Institute of Technology Haifa 3200003 Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stable protein 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
120Populus tremulaMutation(s): 0 
Gene Names: sp1
UniProt
Find proteins for Q9AR79 (Populus tremula)
Explore Q9AR79 
Go to UniProtKB:  Q9AR79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AR79
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.059α = 90
b = 94.372β = 90.22
c = 168.069γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIsrael2028751

Revision History  (Full details and data files)

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