Experimental Data Snapshot

  • Resolution: 0.97 Å

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal structure of oxidized Bacillus pasteurii cytochrome c553 at 0.97-A resolution.

Benini, S.Gonzalez, A.Rypniewski, W.R.Wilson, K.S.Van Beeumen, J.J.Ciurli, S.

(2000) Biochemistry 39: 13115-13126

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • This article reports the first X-ray structure of the soluble form of a c-type cytochrome isolated from a Gram-positive bacterium. Bacillus pasteurii cytochrome c(553), characterized by a low reduction potential and by a low sequence homology with cy ...

    This article reports the first X-ray structure of the soluble form of a c-type cytochrome isolated from a Gram-positive bacterium. Bacillus pasteurii cytochrome c(553), characterized by a low reduction potential and by a low sequence homology with cytochromes from Gram-negative bacteria or eukaryotes, is a useful case study for understanding the structure-function relationships for this class of electron-transfer proteins. Diffraction data on a single crystal of cytochrome c(553) were obtained using synchrotron radiation at 100 K. The structure was determined at 0.97-A resolution using ab initio phasing and independently at 1.70 A in an MAD experiment. In both experiments, the structure solution exploited the presence of a single Fe atom as anomalous scatterer in the protein. For the 0.97-A data, the phasing was based on a single data set. This is the most precise structure of a heme protein to date. The crystallized cytochrome c(553) contains only 71 of the 92 residues expected from the intact protein sequence, lacking the first 21 amino acids at the N-terminus. This feature is consistent with previous evidence that this tail, responsible for anchoring the protein to the cytoplasm membrane, is easily cleaved off during the purification procedure. The heme prosthetic group in B. pasteurii cytochrome c(553) is surrounded by three alpha-helices in a compact arrangement. The largely exposed c-type heme group features a His-Met axial coordination of the Fe(III) ion. The protein is characterized by a very asymmetric charge distribution, with the exposed heme edge located on a surface patch devoid of net charges. A structural search of a representative set of protein structures reveals that B. pasteurii cytochrome c(553) is most similar to Pseudomonas cytochromes c(551), followed by cytochromes c(6), Desulfovibrio cytochrome c(553), cytochromes c(552) from thermophiles, and cytochromes c from eukaryotes. Notwithstanding a low sequence homology, a structure-based alignment of these cytochromes shows conservation of three helical regions, with different additional secondary structure motifs characterizing each protein. In B. pasteurii cytochrome c(553), these motifs are represented by the shortest interhelix connecting fragments observed for this group of proteins. The possible relationships between heme solvent accessibility and the electrochemical reduction potential are discussed.

    Related Citations: 
    • Cytochrome C-553 from the Alkalophilic Bacterium Bacillus Pasteurii Has the Primary Structure Characteristics of a Lipoprotein
      Vandenberghe, I.H.M.,Guisez, Y.,Ciurli, S.,Benini, S.,Van-Beeumen, J.J.
      (1999) Biochem.Biophys.Res.Commun. 264: 380
    • Modulation of Bacillus Pasteurii Cytochrome C553 Reduction Potential by Structural and Solution Parameters
      Benini, S.,Borsari, M.,Ciurli, S.,Dikiy, A.,Lamborghini, M.
      (1998) J.Biol.Inorg.Chem. 3: 371
    • Crystals of Cytochrome C-553 from Bacillus Pasteurii Show Diffraction to 0.97 A Resolution
      Benini, S.,Ciurli, S.,Rypniewski, W.R.,Wilson, K.S.
      (1997) Proteins 28: 580

    Organizational Affiliation

    European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
71Sporosarcina pasteuriiMutation(s): 0 
Find proteins for P82599 (Sporosarcina pasteurii)
Go to UniProtKB:  P82599
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download SDF File 
Download CCD File 
C34 H32 Fe N4 O4
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 0.97 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.144α = 90.00
b = 39.422β = 90.00
c = 44.021γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ARP/wARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description
  • Version 1.4: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description