6SUY

Yeast cytochrome c in complex with an octa-anionic calix[4]arene

• PDB DOI: https://doi.org/10.2210/pdb6SUY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-09-17 Released: 2020-01-15 
• Deposition Author(s): Alex, J.M., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.179 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene.

Alex, J.M., Brancatelli, G., Volpi, S., Bonaccorso, C., Casnati, A., Geremia, S., Crowley, P.B.

(2020) Org Biomol Chem 18: 211-214

• PubMed: 31808772 
• DOI: https://doi.org/10.1039/c9ob02275a
• Primary Citation of Related Structures:  
  6SUY


• PubMed Abstract: 
  

  Sulfonato-calix[n]arenes (sclxn) are promising tools to generate crystalline protein frameworks. We report, for the first time, a lower rim functionalised octa-anionic calix[4]arene (sclx4mc) in complex with proteins. Two crystal structures of sclx4mc bound to yeast or horse heart cytochrome c (cytc) are described. Highly porous honeycomb or tubular assemblies were obtained with yeast or horse cytc, respectively. Related frameworks were obtained previously with sclx8 and sclx6 but not with sclx4, suggesting that the ligand charge is a determining factor.

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Organizational Affiliation: 

School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.8 kDa 
• Atom Count: 2,208 
• Modelled Residue Count: 214 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A, B	108	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044  Go to UniProtKB:  P00044

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LVT (Subject of Investigation/LOI)	D [auth A], K [auth B]	octa-anionic calix[4]arene C36 H32 O24 S4 JUMSFKUQLZLREY-UHFFFAOYSA-N
HEC	C [auth A], J [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	E [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.179 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.489	α = 90
b = 102.489	β = 90
c = 72.18	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Alex, J.M., Crowley, P.B.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/CDA/2168

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary