Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.06 kDa 
• Atom Count: 1504 
• Modelled Residue Count: 178 
• Deposited Residue Count: 178 
• Unique protein chains: 1

1C6O

CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS

• PDB DOI: 10.2210/pdb1C6O/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Tetradesmus obliquus
• Mutation(s): No 


• Deposited: 1999-04-07 Released: 2000-04-12 
• Deposition Author(s): Schnackenberg, J., Than, M.E., Mann, K., Wiegand, G., Huber, R., Reuter, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.213 

Literature

Amino acid sequence, crystallization and structure determination of reduced and oxidized cytochrome c6 from the green alga Scenedesmus obliquus.

Schnackenberg, J., Than, M.E., Mann, K., Wiegand, G., Huber, R., Reuter, W.

(1999) J Mol Biol 290: 1019-1030

• PubMed: 10438600 
• DOI: 10.1006/jmbi.1999.2944
• Primary Citation of Related Structures:  
  1C6O, 1C6R


• PubMed Abstract: 
  

Cytochrome c6from the unicellular green alga Scenedesmus obliquus was sequenced, crystallized in its reduced and oxidized state and the three-dimensional structure of the protein in both redox states was determined by X-ray crystallography. Reduced cytochrome c6crystallized as a monomer in the space group P 21212, whereas the oxidized protein crystallized as a dimer in the space group P 3121. The structures were solved by molecular replacement and refined to 1. 9 and 2.0 A, respectively. Comparison of the structures of both redox states revealed only slight differences on the protein surface, whereas a distortion along the axis between the heme iron and its coordinating Met61 residue was observed. No redox-dependent movement of internal water molecules could be detected. The high degree of similarity of the surfaces and charge distributions of both redox states, as well as the dimerization of cytochrome c6as observed in the oxidized crystal, is discussed with respect to its biological relevance and its implications for the reaction mechanisms between cytochrome c6and its redox partners. The dimer of oxidized cytochrome c6may represent a molecular structure occurring in a binary complex with cytochrome b6f. This assembly might be required for the correct orientation of cytochrome c6with respect to its redox partner cytochrome b6f, facilitating the electron transfer within the complex. If the dimerization is not redox-dependent in vivo, the almost identical surfaces of both redox states do not support a long range differentiation between reduced and oxidized cyt c6, i.e. a random collision model for the formation of an electron transfer complex must be assumed.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, Martinsried, D-82152, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C6	A, B	89	Tetradesmus obliquus	Mutation(s): 0  Gene Names: petJ
UniProt
Find proteins for P57736 (Tetradesmus obliquus) Explore P57736  Go to UniProtKB:  P57736

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.213 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.56	α = 90
b = 49.56	β = 90
c = 152.44	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling
TRUNCATE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-07 
• Released Date: 2000-04-12 
Deposition Author(s): Schnackenberg, J., Than, M.E., Mann, K., Wiegand, G., Huber, R., Reuter, W.

Revision History  

• Version 1.0: 2000-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description