6SUY

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

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
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland. [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1
A, B
108Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LVT (Subject of Investigation/LOI)
Query on LVT
Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]		octa-anionic calix[4]arene
C36 H32 O24 S4
JUMSFKUQLZLREY-UHFFFAOYSA-N
HEC
Query on HEC
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA
Download Ideal Coordinates CCD File 
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 = 102.489α = 90
b = 102.489β = 90
c = 72.18γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/CDA/2168

Revision History  (Full details and data files)

  • 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