7ZS0 | pdb_00007zs0

Diheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Redox potential tuning by calcium ions in a novel c-type cytochrome from an anammox organism.

Akram, M.Hauser, D.Dietl, A.Steigleder, M.Ullmann, G.M.Barends, T.R.M.

(2024) J Biological Chem : 108082-108082

  • DOI: https://doi.org/10.1016/j.jbc.2024.108082
  • Primary Citation of Related Structures:  
    7ZS0, 7ZS1, 7ZS2, 9FBK

  • PubMed Abstract: 

    The electrochemical potentials of redox-active proteins need to be tuned accurately to the correct values for proper biological function. Here we describe a diheme cytochrome c with high heme redox potentials of about +350 mV, despite having a large overall negative charge which typically reduces redox potentials. High resolution crystal structures, spectroelectrochemical measurements and high-end computational methods show how this is achieved: each heme iron has a calcium cation positioned next to it at a distance of only 6.9 Å, raising their redox potentials by several hundred mV through electrostatic interaction. We suggest that this has evolved to provide the protein with a high redox potential despite its large negative surface charge, which it likely requires for interactions with redox partners.


  • Organizational Affiliation
    • Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical (Diheme) protein316Candidatus KueneniaMutation(s): 0 
Gene Names: KsCSTR_07890KSMBR1_1466kustd1711
UniProt
Find proteins for Q1PZE6 (Kuenenia stuttgartiensis)
Explore Q1PZE6 
Go to UniProtKB:  Q1PZE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1PZE6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.92α = 90
b = 92.29β = 90
c = 54.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-12-25
    Changes: Database references
  • Version 1.3: 2025-01-22
    Changes: Database references