3CP5 | pdb_00003cp5

Cytochrome c from rhodothermus marinus

• PDB DOI: https://doi.org/10.2210/pdb3CP5/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rhodothermus marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-31 Released: 2008-10-28 
• Deposition Author(s): Stelter, M., Melo, A., Saraiva, L., Teixeira, M., Archer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.174 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.135 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Literature

A novel type of monoheme cytochrome c: biochemical and structural characterization at 1.23 A resolution of rhodothermus marinus cytochrome c

Stelter, M., Melo, A.M., Pereira, M.M., Gomes, C.M., Hreggvidsson, G.O., Hjorleifsdottir, S., Saraiva, L.M., Teixeira, M., Archer, M.

(2008) Biochemistry 47: 11953-11963

• PubMed: 18855424 
• DOI: https://doi.org/10.1021/bi800999g
• Primary Citation Related Structures: 
  3CP5


• PubMed Abstract: 
  

  Monoheme cytochromes of the C-type are involved in a large number of electron transfer processes, which play an essential role in multiple pathways, such as respiratory chains, either aerobic or anaerobic, and the photosynthetic electron transport chains. This study reports the biochemical characterization and the crystallographic structure, at 1.23 A resolution, of a monoheme cytochrome c from the thermohalophilic bacterium Rhodothermus marinus. In addition to an alpha-helical core folded around the heme, common for this type of cytochrome, the X-ray structure reveals one unusual alpha-helix and a unique N-terminal extension, which wraps around the back of the molecule. Based on a thorough structural and amino acid sequence comparison, we propose R. marinus cytochrome c as the first characterized member of a new class of C-type cytochromes.

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Organizational Affiliation: 
• Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.55 kDa 
• Atom Count: 1,167 
• Modeled Residue Count: 116 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A	124	Rhodothermus marinus	Mutation(s): 0  Gene Names: cytC
UniProt
Find proteins for B3FQS5 (Rhodothermus marinus) Explore B3FQS5  Go to UniProtKB:  B3FQS5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.174 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.135 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.592	α = 90
b = 32.644	β = 94.56
c = 42.064	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MxCuBE	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Stelter, M., Melo, A., Saraiva, L., Teixeira, M., Archer, M.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary