2B4Z | pdb_00002b4z

Crystal structure of cytochrome C from bovine heart at 1.5 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2B4Z/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2005-09-27 Released: 2005-10-11 
• Deposition Author(s): Mirkin, N., Jakoncic, J., Stojanoff, V., Moreno, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

High resolution X-ray crystallographic structure of bovine heart cytochrome c and its application to the design of an electron transfer biosensor.

Mirkin, N., Jaconcic, J., Stojanoff, V., Moreno, A.

(2008) Proteins 70: 83-92

• PubMed: 17634981 
• DOI: https://doi.org/10.1002/prot.21452
• Primary Citation Related Structures: 
  2B4Z


• PubMed Abstract: 
  

  Cytochrome c is one of the most studied proteins probably due to its electron-transfer properties in aerobic and anaerobic respiration. Particularly, cytochrome c from bovine heart is a small protein, M(r) 12,230 Da, globular (hydrodynamic diameter of 3.4 nm), soluble in different buffer solutions, and commercially available. Despite being a quite well-studied protein and relatively easy to manipulate from the biochemical and electrochemical viewpoint, its 3D structure has never been published. In this work, the purification, crystallization and 3D structure of one of the cytochrome c isoforms is presented to 1.5 A resolution. It is also shown how the presence of isoforms made both the purification and crystallization steps difficult. Finally, a new approach for protein electrocrystallization and design of biosensors is presented.

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Organizational Affiliation: 
• Hunter College, City University of New York, New York, New York, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.21 kDa 
• Atom Count: 1,079 
• Modeled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A	104	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P62894 (Bos taurus) Explore P62894  Go to UniProtKB:  P62894

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.84	α = 90
b = 54.48	β = 90
c = 55.33	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-11 
Deposition Author(s): Mirkin, N., Jakoncic, J., Stojanoff, V., Moreno, A.

Revision History  

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description