6Z5M | pdb_00006z5m

The RSL - sulfonato-calix[8]arene complex, I23 form, Gly-HCl pH 2.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EVBClick on this verticalbar to view details

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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.611α = 90
b = 103.611β = 90
c = 103.611γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EVBClick on this verticalbar to view details

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: Data collection, Database references, Refinement description