8C9Z | pdb_00008c9z

The RSL - sulfonato-calix[8]arene complex, H32 form, citrate pH 6.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Protein-macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin-sulfonato-calix[8]arene complex.

Mockler, N.M.Ramberg, K.O.Crowley, P.B.

(2023) Acta Crystallogr D Struct Biol 79: 624-631

  • DOI: https://doi.org/10.1107/S2059798323003832
  • Primary Citation of Related Structures:  
    8C9Y, 8C9Z

  • PubMed Abstract: 

    Controlled protein assembly and crystallization is necessary as a means of generating diffraction-quality crystals as well as providing a basis for new types of biomaterials. Water-soluble calixarenes are useful mediators of protein crystallization. Recently, it was demonstrated that Ralstonia solanacearum lectin (RSL) co-crystallizes with anionic sulfonato-calix[8]arene (sclx 8 ) in three space groups. Two of these co-crystals only grow at pH ≤ 4 where the protein is cationic, and the crystal packing is dominated by the calixarene. This paper describes a fourth RSL-sclx 8 co-crystal, which was discovered while working with a cation-enriched mutant. Crystal form IV grows at high ionic strength in the pH range 5-6. While possessing some features in common with the previous forms, the new structure reveals alternative calixarene binding modes. The occurrence of C 2 -symmetric assemblies, with the calixarene at special positions, appears to be an important result for framework fabrication. Questions arise regarding crystal screening and exhaustive searching for polymorphs.


  • Organizational Affiliation

    School of Biological and Chemical Sciences, University of 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVB (Subject of Investigation/LOI)
Query on EVB

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
sulfonato-calix[8]arene
C56 H48 O32 S8
KCEGJGDGMRAJEP-UHFFFAOYSA-N
BDF
Query on BDF

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
beta-D-fructopyranose
C6 H12 O6
LKDRXBCSQODPBY-ARQDHWQXSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.114α = 90
b = 76.114β = 90
c = 113.649γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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
Irish Research CouncilIrelandGOIPG/2021/333
Science Foundation IrelandIreland13/CDA/2168
Science Foundation IrelandIreland12/RC/2275_P2

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection