4YE1 | pdb_00004ye1

A cytochrome c plus calixarene structure - alternative ligand binding mode

• PDB DOI: https://doi.org/10.2210/pdb4YE1/pdb

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


• Deposited: 2015-02-23 Released: 2015-05-13 
• Deposition Author(s): Mallon, M.M., McGovern, R.E., McCarty, A.A., Crowley, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.160 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.130 (Depositor) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

A cytochrome c-calixarene structure

Mallon, M.M., McGovern, R.E., McCarty, 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: 27.65 kDa 
• Atom Count: 2,465 
• Modeled 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, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044  Go to UniProtKB:  P00044

Small Molecules

Ligands 3 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
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.160 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.130 (Depositor) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.85	α = 90
b = 56.07	β = 90
c = 108.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Mallon, M.M., McGovern, R.E., McCarty, A.A., Crowley, P.B.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary