1U75

Electron Transfer Complex between Horse Heart Cytochrome c and Zinc-Porphyrin Substituted Cytochrome c Peroxidase

• PDB DOI: https://doi.org/10.2210/pdb1U75/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae, Equus caballus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-02 Released: 2004-09-28 
• Deposition Author(s): Crane, B.R., Kang, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.306 
• R-Value Work: 0.271 
• R-Value Observed: 0.273 

Starting Model: experimental

Literature

Electron transfer between cytochrome c and cytochome c peroxidase in single crystals.

Kang, S.A., Marjavaara, P.J., Crane, B.R.

(2004) J Am Chem Soc 126: 10836-10837

• PubMed: 15339156 
• DOI: https://doi.org/10.1021/ja049230u
• Primary Citation of Related Structures:  
  1U74, 1U75


• PubMed Abstract: 
  

  Cytochrome c (Cc) and cytochrome c peroxidase (CcP) form an important redox pair for understanding interprotein electron transfer (ET). Measurements of ET rates from photoexcited CcP substituted with Zn porphyrin to either yeast Fe(III)Cc or horse Fe(III)Cc in crystals reveal that the molecular associations found in the respective crystal structures determine solution reactivity. Similar forward rates for yeast isozyme-1 Cc (yCc) and yCc homologue horse Cc (hCc), despite different orientations relative to CcP, suggest small-amplitude conformational gating of ET even in the crystalline state; faster back ET in the yCc compared to the hCc complex agrees with the relative coupling between redox sites predicted by the structures.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.33 kDa 
• Atom Count: 6,032 
• Modelled Residue Count: 693 
• Deposited Residue Count: 696 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c peroxidase	A, C	296	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: Yeast EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431  Go to UniProtKB:  P00431

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	B	104	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P00004 (Equus caballus) Explore P00004  Go to UniProtKB:  P00004

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZNH	E [auth A], H [auth C]	PROTOPORPHYRIN IX CONTAINING ZN C34 H32 N4 O4 Zn FUTVBRXUIKZACV-RGGAHWMASA-L
HEC	F [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
PO4	D [auth A], G [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.306 
• R-Value Work: 0.271 
• R-Value Observed: 0.273 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.465	α = 90
b = 104.465	β = 90
c = 186.884	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Crane, B.R., Kang, S.A.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2021-03-03
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description