8R3D | pdb_00008r3d

Crystal structure of Pent only at pH 8.8

• PDB DOI: https://doi.org/10.2210/pdb8R3D/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Enterobacteria phage L1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-08 Released: 2024-03-06 
• Deposition Author(s): Flood, R.J., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Multivalent Calixarene Complexation of a Designed Pentameric Lectin.

Flood, R.J., Cerofolini, L., Fragai, M., Crowley, P.B.

(2024) Biomacromolecules 25: 1303-1309

• PubMed: 38227741 
• DOI: https://doi.org/10.1021/acs.biomac.3c01280
• Primary Citation Related Structures: 
  8R3B, 8R3C, 8R3D


• PubMed Abstract: 
  

  We describe complex formation between a designed pentameric β-propeller and the anionic macrocycle sulfonato-calix[8]arene ( sclx ₈ ), as characterized by X-ray crystallography and NMR spectroscopy. Two crystal structures and ¹⁵ N HSQC experiments reveal a single calixarene binding site in the concave pocket of the β-propeller toroid. Despite the symmetry mismatch between the pentameric protein and the octameric macrocycle, they form a high affinity multivalent complex, with the largest protein-calixarene interface observed to date. This system provides a platform for investigating multivalency.

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Organizational Affiliation: 
• SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.
Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy.
Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy.
Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto, Fiorentino, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.75 kDa 
• Atom Count: 2,183 
• Modeled Residue Count: 235 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta propeller	A, B, C, D, E	48	Enterobacteria phage L1	Mutation(s): 0
UniProt
Find proteins for A0A140UHM9 (Enterobacteria phage L1) Explore A0A140UHM9  Go to UniProtKB:  A0A140UHM9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.74	α = 90
b = 59.131	β = 90
c = 72.464	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Flood, R.J., Crowley, P.B.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	12/RC/2275_P2

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release