1KIB

cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in the form of an oblate shell

• PDB DOI: https://doi.org/10.2210/pdb1KIB/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Limnospira maxima
• Mutation(s): No 


• Deposited: 2001-12-03 Released: 2002-07-03 
• Deposition Author(s): Kerfeld, C.A., Sawaya, M.R., Krogmann, D., Yeates, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell.

Kerfeld, C.A., Sawaya, M.R., Krogmann, D.W., Yeates, T.O.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1104-1110

• PubMed: 12077429 
• DOI: https://doi.org/10.1107/s0907444902006534
• Primary Citation of Related Structures:  
  1KIB


• PubMed Abstract: 
  

  Cytochrome c(6) from the cyanobacterium Arthrospira maxima is present in isoforms that can be resolved by size-exclusion chromatography. One isoform crystallized in space group I4(1)32 with eight protein molecules in the asymmetric unit and a total of 384 molecules in the unit cell. Within the crystal, the molecules are arranged as clusters of 24 cytochrome c(6) molecules. Each cluster is a hollow shell with approximate octahedral (432) symmetry. Structural and biochemical studies of cytochrome c(6) isolated from other cyanobacteria and algae have led to the suggestion that cytochrome c(6) forms oligomers. The cytochrome c(6) complex described here is the largest assembly of cytochrome c(6) molecules observed thus far.

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Organizational Affiliation: 

Molecular Biology Institute, University of California, Los Angeles, Box 951570, 90095-1570, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.92 kDa 
• Atom Count: 5,524 
• Modelled Residue Count: 712 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c6	A, B, C, D, E, F, G, H	89	Limnospira maxima	Mutation(s): 0
UniProt
Find proteins for P00118 (Limnospira maxima) Explore P00118  Go to UniProtKB:  P00118

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 237	α = 90
b = 237	β = 90
c = 237	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-03 
Deposition Author(s): Kerfeld, C.A., Sawaya, M.R., Krogmann, D., Yeates, T.O.

Revision History  

• Version 1.0: 2002-07-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-03-03
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description