4N0K

Atomic resolution crystal structure of a cytochrome c-calixarene complex

• PDB DOI: https://doi.org/10.2210/pdb4N0K/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-10-02 Released: 2014-09-10 
• Deposition Author(s): McGovern, R.E., Pye, V.E., Crowley, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.180 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

A cytochrome c-calixarene structure at atomic resolution

McGovern, R.E., McCarthy, A.A., Crowley, P.B.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.56 kDa 
• Atom Count: 2,435 
• Modelled Residue Count: 216 
• 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 S288C	Mutation(s): 1  Gene Names: CYC1, J1653, YJR048W
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044  Go to UniProtKB:  P00044

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T3Y	D [auth A], F [auth B], G [auth B]	25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid C28 H24 O16 S4 JFYBCAFLVNKHHG-UHFFFAOYSA-N
HEC	C [auth A], E [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.180 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.11	α = 90
b = 55.78	β = 90
c = 119.08	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): McGovern, R.E., Pye, V.E., Crowley, P.B.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 2.0: 2021-03-10
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary