6S8Y | pdb_00006s8y

Crystal structure of cytochrome c in complex with a sulfonated quinoline-derived foldamer

• PDB DOI: https://doi.org/10.2210/pdb6S8Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-10 Released: 2019-09-25 
• Deposition Author(s): Alex, J.M., Corvaglia, V., Hu, X., Engilberge, S., Huc, I., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.267 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a protein-aromatic foldamer composite: macromolecular chiral resolution.

Alex, J.M., Corvaglia, V., Hu, X., Engilberge, S., Huc, I., Crowley, P.B.

(2019) Chem Commun (Camb) 55: 11087-11090

• PubMed: 31460523 
• DOI: https://doi.org/10.1039/c9cc05330a
• Primary Citation Related Structures: 
  6S8Y


• PubMed Abstract: 
  

  Co-crystallization of a 2 kDa tether-free sulfonated foldamer and the 13 kDa lysine-rich cytochrome c yielded a remarkable biohybrid assembly with chiral resolution of the foldamer helix handedness. In the crystal a ∼5 nm foldamer stack was surrounded by eight molecules of protein. NMR and CD experiments suggest interesting differences in the solution state recognition processes.

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Organizational Affiliation: 
• School of Chemistry, National University of Ireland, University Road, Galway, H91 TK33, Ireland.
Universite de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Europeen de Chimie et Biologie, 2 Rue Escarpit, Pessac 33600, France and Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstraße 5-13, München 81377, Germany. [e-mail] [e-mail].
Universite de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Europeen de Chimie et Biologie, 2 Rue Escarpit, Pessac 33600, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.01 kDa 
• Atom Count: 1,350 
• Modeled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A	107	Saccharomyces cerevisiae	Mutation(s): 0  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
L0T (Subject of Investigation/LOI)	G [auth A], H [auth A]	8-acetamido-2-[[2-[[2-[[2-[[2-[[2-[[2-[(2-carboxy-4-sulfonato-quinolin-8-yl)carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]quinoline-4-sulfonate C82 H44 N16 O34 S8 IHZXKZSCEKIUSH-UHFFFAOYSA-F
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
ZN	C [auth A], D [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.267 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.138	α = 90
b = 39.138	β = 90
c = 187.366	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Alex, J.M., Corvaglia, V., Hu, X., Engilberge, S., Huc, I., Crowley, P.B.

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

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary