2CTH | pdb_00002cth

CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH

• PDB DOI: https://doi.org/10.2210/pdb2CTH/pdb
• Entry: 2CTH supersedes: 1CTH
• BMRB: 5625

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): No 


• Deposited: 1997-06-18 Released: 1997-12-24 
• 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: 1.67 Å
• R-Value Free: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.31 kDa 
• Atom Count: 2,088 
• Modeled Residue Count: 214 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C3	A, B	107	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0
UniProt
Find proteins for P00131 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P00131  Go to UniProtKB:  P00131

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.190 (Depositor) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.3	α = 90
b = 77.3	β = 90
c = 77.1	γ = 120

Software Package:

Software Name	Purpose
SHELXL-93	model building
SHELXL-93	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXL-93	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-24 
Deposition Author(s): Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.
• This entry supersedes: 1CTH

Revision History  

• Version 1.0: 1997-12-24
  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: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary