7ZS2 | pdb_00007zs2

Diheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis, M292H mutant

• PDB DOI: https://doi.org/10.2210/pdb7ZS2/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Candidatus Kuenenia
• Expression System: Shewanella oneidensis MR-1
• Mutation(s): Yes 


• Deposited: 2022-05-05 Released: 2023-05-17 
• Deposition Author(s): Akram, M., Barends, T.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.126 (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 : 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: 35.77 kDa 
• Atom Count: 2,808 
• 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): 1  Gene Names: KsCSTR_07890, KSMBR1_1466, kustd1711
UniProt
Find proteins for Q1PZE6 (Kuenenia stuttgartiensis) Explore Q1PZE6  Go to UniProtKB:  Q1PZE6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	F [auth A], G [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
IMD	H [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.65	α = 90
b = 92.71	β = 90
c = 55.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Akram, M., Barends, T.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Refinement description
• Version 2.0: 2024-09-04
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 2.1: 2024-10-23
  Changes: Structure summary
• Version 2.2: 2024-12-25
  Changes: Database references
• Version 2.3: 2025-01-22
  Changes: Database references