3CYR

CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774P

• PDB DOI: https://doi.org/10.2210/pdb3CYR/pdb
• Entry: 3CYR supersedes: 2CYR

• Classification: ELECTRON TRANSPORT
• Organism(s): Desulfovibrio desulfuricans
• Mutation(s): No 


• Deposited: 1997-07-24 Released: 1998-01-28 
• Deposition Author(s): Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.221 (Depositor) 
• R-Value Work: 
  0.160 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstroms Resolution

Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.

(1998) Inorganica Chim Acta 273: 213-224

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.06 kDa 
• Atom Count: 1,061 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C3	A	107	Desulfovibrio desulfuricans	Mutation(s): 0
UniProt
Find proteins for Q9L915 (Desulfovibrio desulfuricans) Explore Q9L915  Go to UniProtKB:  Q9L915

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.221 (Depositor) 
• R-Value Work:  0.160 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.71	α = 90
b = 62.71	β = 90
c = 111.09	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.
• This entry supersedes: 2CYR

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary