1C53

S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD

• PDB DOI: https://doi.org/10.2210/pdb1C53/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
• Mutation(s): No 


• Deposited: 1991-08-26 Released: 1993-10-31 
• Deposition Author(s): Nakagawa, A., Higuchi, Y., Yasuoka, N., Katsube, Y., Yaga, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.194 

Literature

S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.

Nakagawa, A., Higuchi, Y., Yasuoka, N., Katsube, Y., Yagi, T.

(1990) J Biochem 108: 701-703

• PubMed: 1964450 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a123267
• Primary Citation of Related Structures:  
  1C53


• PubMed Abstract: 
  

  The three-dimensional structure of cytochrome c-553 isolated from sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki F strain, has been determined by the multi-wavelength anomalous dispersion technique with use of synchrotron radiation. The result shows that bacterial S-class cytochromes c have a variety of folding patterns. The relative location of two a-helices at amino- and carboxyl-terminals and the style of bonding to the heme group show "cytochrome c folding," but other regions of the structure are different from those of other cytochromes c previously reported. The results also give useful information about the location of sulfate-reducing bacterium on the phylogenetic tree of the bacterial cytochromes c superfamily.

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Organizational Affiliation: 

Photon Factory, National Laboratory for High Energy Physics, Hyogo.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.03 kDa 
• Atom Count: 122 
• Modelled Residue Count: 79 
• Deposited Residue Count: 79 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C553	A	79	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 0
UniProt
Find proteins for P00120 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P00120  Go to UniProtKB:  P00120

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.194 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 42.7	β = 90
c = 103.4	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Nakagawa, A., Higuchi, Y., Yasuoka, N., Katsube, Y., Yaga, T.

Revision History  

• Version 1.0: 1993-10-31
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other