6Z60

The RSL - sulfonato-calix[8]arene complex, P213 form, CAPS pH 9.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Facile Fabrication of Protein-Macrocycle Frameworks.

Ramberg, K.O.Engilberge, S.Skorek, T.Crowley, P.B.

(2021) J Am Chem Soc 143: 1896-1907

  • DOI: https://doi.org/10.1021/jacs.0c10697
  • Primary Citation of Related Structures:  
    6Z5G, 6Z5M, 6Z5P, 6Z5Q, 6Z5W, 6Z5X, 6Z5Z, 6Z60, 6Z62, 7ALF, 7ALG

  • PubMed Abstract: 

    Precisely defined protein aggregates, as exemplified by crystals, have applications in functional materials. Consequently, engineered protein assembly is a rapidly growing field. Anionic calix[n]arenes are useful scaffolds that can mold to cationic proteins and induce oligomerization and assembly. Here, we describe protein-calixarene composites obtained via cocrystallization of commercially available sulfonato-calix[8]arene ( sclx 8 ) with the symmetric and "neutral" protein RSL. Cocrystallization occurred across a wide range of conditions and protein charge states, from pH 2.2-9.5, resulting in three crystal forms. Cationization of the protein surface at pH ∼ 4 drives calixarene complexation and yielded two types of porous frameworks with pore diameters >3 nm. Both types of framework provide evidence of protein encapsulation by the calixarene. Calixarene-masked proteins act as nodes within the frameworks, displaying octahedral-type coordination in one case. The other framework formed millimeter-scale crystals within hours, without the need for precipitants or specialized equipment. NMR experiments revealed macrocycle - modulated side chain p K a values and suggested a mechanism for pH-triggered assembly. The same low pH framework was generated at high pH with a permanently cationic arginine-enriched RSL variant. Finally, in addition to protein framework fabrication, sclx 8 enables de novo structure determination.


  • 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
Fucose-binding lectin protein90Ralstonia solanacearumMutation(s): 0 
Gene Names: E7Z57_08365RSP795_21825RSP822_19650RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum)
Explore A0A0S4TLR1 
Go to UniProtKB:  A0A0S4TLR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TLR1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.872α = 90
b = 63.872β = 90
c = 63.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
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

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description