7AH0

Crystal structure of the de novo designed two-heme binding protein, 4D2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

An expandable, modular de novo protein platform for precision redox engineering.

Hutchins, G.H.Noble, C.E.M.Bunzel, H.A.Williams, C.Dubiel, P.Yadav, S.K.N.Molinaro, P.M.Barringer, R.Blackburn, H.Hardy, B.J.Parnell, A.E.Landau, C.Race, P.R.Oliver, T.A.A.Koder, R.L.Crump, M.P.Schaffitzel, C.Oliveira, A.S.F.Mulholland, A.J.Anderson, J.L.R.

(2023) Proc Natl Acad Sci U S A 120: e2306046120-e2306046120

  • DOI: https://doi.org/10.1073/pnas.2306046120
  • Primary Citation of Related Structures:  
    7AH0, 8CCR

  • PubMed Abstract: 

    The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo diheme "maquette" protein, 4D2, which we subsequently use to create an expanded, modular platform for heme protein design. A well-folded monoheme variant was created by computational redesign, which was then utilized for the experimental validation of continuum electrostatic redox potential calculations. This demonstrates how fundamental biophysical properties can be predicted and fine-tuned. 4D2 was then extended into a tetraheme helical bundle, representing a 7 nm molecular wire. Despite a molecular weight of only 24 kDa, electron cryomicroscopy illustrated a remarkable level of detail, indicating the positioning of the secondary structure and the heme cofactors. This robust, expressible, highly thermostable and readily designable modular platform presents a valuable resource for redox protein design and the future construction of artificial electron-conducting circuitry.


  • Organizational Affiliation

    School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4D2112synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.213 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.25α = 90
b = 81.25β = 90
c = 59.06γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
SHELXDEphasing
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M02315X/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2023-03-01
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-08-09
    Changes: Database references