9FBK | pdb_00009fbk

Diheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis, without glycerol cryoprotectant

• PDB DOI: https://doi.org/10.2210/pdb9FBK/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Candidatus Kuenenia
• Expression System: Shewanella oneidensis MR-1
• Mutation(s): No 


• Deposited: 2024-05-14 Released: 2024-12-25 
• Deposition Author(s): Hauser, D., Barends, T.R.M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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 301: 108082-108082

• PubMed: 39675707 
• DOI: https://doi.org/10.1016/j.jbc.2024.108082
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany.
Computational Biochemistry Group, Fakultät für Chemie, Biologie und Geowissenschaften, Universitätsstrasse 30, D-95447 Bayreuth, Germany. Electronic address: [e-mail].
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.73 kDa 
• Atom Count: 2,598 
• Modeled Residue Count: 278 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical (Diheme) protein	A	316	Candidatus Kuenenia	Mutation(s): 0  Gene Names: KsCSTR_07890, KSMBR1_1466, kustd1711
UniProt
Find proteins for Q1PZE6 (Kuenenia stuttgartiensis) Explore Q1PZE6  Go to UniProtKB:  Q1PZE6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	G [auth A], H [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.6	α = 90
b = 92.1	β = 90
c = 55.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Hauser, D., Barends, T.R.M.

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Funding Organization	Location	Grant Number
Other government	Germany	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references
• Version 1.2: 2025-02-05
  Changes: Database references