1GWS | pdb_00001gws

hexadecaheme high molecular weight cytochrome Hmc from Desulfovibrio vulgaris Hildenborough

• PDB DOI: https://doi.org/10.2210/pdb1GWS/pdb

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


• Deposited: 2002-03-25 Released: 2003-02-13 
• Deposition Author(s): Czjzek, M., Haser, R., Bruschi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.276 (Depositor) 
• R-Value Work: 
  0.201 (Depositor) 

Literature

The Crystal Structure of the Hexadaca-Heme Cytochrome Hmc and a Structural Model of its Complex with Cytochrome C3

Czjzek, M., Elantak, L., Zamboni, V., Morelli, X., Dolla, A., Guerlesquin, F., Bruschi, M.

(2002) Structure 10: 1677

• PubMed: 12467575 
• DOI: https://doi.org/10.1016/s0969-2126(02)00909-7
• Primary Citation Related Structures: 
  1GWS


• PubMed Abstract: 
  

  Sulfate-reducing bacteria contain a variety of multi-heme c-type cytochromes. The cytochrome of highest molecular weight (Hmc) contains 16 heme groups and is part of a transmembrane complex involved in the sulfate respiration pathway. We present the 2.42 A resolution crystal structure of the Desulfovibrio vulgaris Hildenborough cytochrome Hmc and a structural model of the complex with its physiological electron transfer partner, cytochrome c(3), obtained by NMR restrained soft-docking calculations. The Hmc is composed of three domains, which exist independently in different sulfate-reducing species, namely cytochrome c(3), cytochrome c(7), and Hcc. The complex involves the last heme at the C-terminal region of the V-shaped Hmc and heme 4 of cytochrome c(3), and represents an example for specific cytochrome-cytochrome interaction.

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Organizational Affiliation: 
• Architecture et Fonction des Macromolécules Biologiques, IBSM-CNRS et Université Aix-Marseille I et II, 31 Chemin Joseph-Aiguier, 13402 Marseille cedex 20, France. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 68.91 kDa 
• Atom Count: 4,631 
• Modeled Residue Count: 503 
• Deposited Residue Count: 545 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIGH-MOLECULAR-WEIGHT CYTOCHROME C	A	545	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0
UniProt
Find proteins for P24092 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P24092  Go to UniProtKB:  P24092

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.276 (Depositor) 
• R-Value Work:  0.201 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.386	α = 90
b = 108.386	β = 90
c = 102.809	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-13 
Deposition Author(s): Czjzek, M., Haser, R., Bruschi, M.

Revision History  

• Version 1.0: 2003-02-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2019-09-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary