1CXC | pdb_00001cxc

CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS

• PDB DOI: https://doi.org/10.2210/pdb1CXC/pdb

• Classification: ELECTRON TRANSPORT (CYTOCHROME)
• Organism(s): Cereibacter sphaeroides
• Mutation(s): No 


• Deposited: 1994-02-14 Released: 1995-09-15 
• Deposition Author(s): Axelrod, H.L., Feher, G., Allen, J.P., Chirino, A.J., Day, M.W., Hsu, B.T., Rees, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 
  0.212 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystallization and X-ray structure determination of cytochrome c2 from Rhodobacter sphaeroides in three crystal forms.

Axelrod, H.L., Feher, G., Allen, J.P., Chirino, A.J., Day, M.W., Hsu, B.T., Rees, D.C.

(1994) Acta Crystallogr D Biol Crystallogr 50: 596-602

• PubMed: 15299423 
• DOI: https://doi.org/10.1107/S0907444994001319
• Primary Citation Related Structures: 
  1CXA, 1CXC, 2CXB


• PubMed Abstract: 
  

  Cytochrome c(2) serves as the secondary electron donor that reduces the photo-oxidized bacteriochlorophyll dimer in photosynthetic bacteria. Cytochrome c(2) from Rhodobacter sphaeroides has been crystallized in three different forms. At high ionic strength, crystals of a hexagonal space group (P6(1)22) were obtained, while at low ionic strength, triclinic (P1) and tetragonal (P4(1)2(1)2) crystals were formed. The three-dimensional structures of the cytochrome in all three crystal forms have been determined by X-ray diffraction at resolutions of 2.20 A (hexagonal), 1.95 A, (triclinic) and 1.53 A (tetragonal). The most significant difference observed was the binding of an imidazole molecule to the iron atom of the heme group in the hexagonal structure. This binding displaces the sulfur atom of Met l00, which forms the axial ligand in the triclinic and tetragonal structures.

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Organizational Affiliation: 
• Department of Physics, University of California, San Diego, La Jolla 92093-0319, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.11 kDa 
• Atom Count: 986 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C2	A	124	Cereibacter sphaeroides	Mutation(s): 0
UniProt
Find proteins for P0C0X8 (Cereibacter sphaeroides) Explore P0C0X8  Go to UniProtKB:  P0C0X8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work:  0.212 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.33	α = 90
b = 82.33	β = 90
c = 37.61	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-09-15 
Deposition Author(s): Axelrod, H.L., Feher, G., Allen, J.P., Chirino, A.J., Day, M.W., Hsu, B.T., Rees, D.C.

Revision History  

• Version 1.0: 1995-09-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2021-03-03
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary