5NCV | pdb_00005ncv

Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene

• PDB DOI: https://doi.org/10.2210/pdb5NCV/pdb

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


• Deposited: 2017-03-06 Released: 2018-03-14 
• Deposition Author(s): Alex, J.M., Rennie, M.L., Crowley, P.B.
• Funding Organization(s): Science Funding Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Phosphonated Calixarene as a ""Molecular Glue"" for Protein Crystallization

Alex, J.M., Rennie, M.L., Volpi, S., Sansone, F., Casnati, A., Crowley, P.B.

(2018) Cryst Growth Des 18: 2467-2473

• DOI: https://doi.org/10.1021/acs.cgd.8b00092

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.76 kDa 
• Atom Count: 2,303 
• Modeled Residue Count: 208 
• 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
8TE	D [auth A], E [auth A], H [auth B]	p-Methylphosphonatocalix[4]arene C32 H36 O16 P4 HXGDFDVLRPRMJW-UHFFFAOYSA-N
HEC	C [auth A], G [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.917	α = 90
b = 80.227	β = 93.07
c = 47.807	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Alex, J.M., Rennie, M.L., Crowley, P.B.

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

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-03-28
  Changes: Data collection, Database references
• Version 1.2: 2018-11-14
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary