9FRO | pdb_00009fro

Crystal structure of Pent - p-sulfonatocalix[6]arene complex

PDB DOI: https://doi.org/10.2210/pdb9FRO/pdb

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

Deposited: 2024-06-19 Released: 2024-12-04
Deposition Author(s): Flood, R.J., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A Macrocycle-Mediated Protein Cage.

Flood, R.J., Thureau, A., Crowley, P.B.

(2024) ACS Macro Lett 13: 1686-1690

PubMed: 39592260 Search on PubMed
DOI: https://doi.org/10.1021/acsmacrolett.4c00656
Primary Citation Related Structures:
9FRO

PubMed Abstract:
Engineered protein cages are of great interest considering their diverse applications in delivery and catalysis. Here, we describe macrocycle-triggered icosahedral cage assembly of a designed β-propeller. Cage assembly was evidenced by small-angle X-ray scattering and X-ray crystallography.

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.

Macromolecule Content

Total Structure Weight: 31.97 kDa
Atom Count: 2,341
Modeled Residue Count: 236
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta propeller	A, B, C [auth E], D, E [auth C]	48	Enterobacteria phage L1	Mutation(s): 0
UniProt
Find proteins for A0A140UHM9 (Enterobacteria phage L1) Explore A0A140UHM9 Go to UniProtKB: A0A140UHM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A140UHM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FWQ (Subject of Investigation/LOI) Query on FWQ Download:Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain H [auth E] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain H [auth E] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	H [auth E], J [auth D], K [auth D], L [auth D]	p-sulfonatocalix[6]arene C₄₂ H₃₀ O₂₄ S₆ BXOUPTJVBGEDIR-UHFFFAOYSA-H		Interactions Focus chain H [auth E] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain H [auth E] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D]
NDG Query on NDG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth D] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth D] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth D] mmCIF format, chain M [auth C]	F [auth A], G [auth B], I [auth D], M [auth C]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth D] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth D] Focus chain M [auth C]