7BAD

Crystal structure of PAFB in complex with p-sulfonato-calix[8]arene and zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Porous assembly of an antifungal protein mediated by zinc and sulfonato-calix[8]arene.

Guagnini, F.Huber, A.Alex, J.M.Marx, F.Crowley, P.B.

(2021) J Struct Biol 213: 107711-107711

  • DOI: https://doi.org/10.1016/j.jsb.2021.107711
  • Primary Citation of Related Structures:  
    7BAD, 7BAE, 7BAF

  • PubMed Abstract: 

    Controlled protein assembly holds great potential in the fabrication of biohybrid materials. However, the structural diversity and complexity of proteins present an obstacle to controlled assembly. Supramolecular chemistry is a possible solution as it offers tools to mediate self-assembly with molecular precision. This paper deals with the calixarene- and zinc-mediated assembly and crystallization of the histidine-rich Penicillium chrysogenum antifungal protein B (PAFB). We report crystal structures of pure PAFB, PAFB in complex with Zn 2+ , and the ternary complex of PAFB, Zn 2+ and sulfonato-calix[8]arene (sclx 8 ). A comparison of the three crystal structures revealed the structural plasticity of PAFB. While the flexible and highly anionic sclx 8 resulted in large molecular weight aggregates of PAFB in solution, diffraction-quality crystals of PAFB-sclx 8 were not obtained. We report crystals of PAFB-Zn 2+ -sclx 8 in which a trinuclear zinc cluster occurred adjacent to a calixarene binding site. Interestingly, the combination of sclx 8 complexation and zinc coordination resulted in a porous framework with channels of circa 2 nm diameter. Detailed analysis of the crystal structure highlighted novel molecular recognition features. This research enriches the set of supramolecular interactions available to promote protein assembly.


  • Organizational Affiliation

    School of Chemistry, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antifungal protein58Penicillium rubens Wisconsin 54-1255Mutation(s): 0 
Gene Names: afpPc12g08290
UniProt
Find proteins for B6GXZ8 (Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255))
Explore B6GXZ8 
Go to UniProtKB:  B6GXZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6GXZ8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.175α = 90
b = 101.175β = 90
c = 46.303γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
pointlessdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/CDA/2168
Irish Research CouncilIrelandGOIPD/2019/513

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description