9HI3 | pdb_00009hi3

C-terminal domain of pectobacterial FusB in complex with spinach ferredoxin 1

• PDB DOI: https://doi.org/10.2210/pdb9HI3/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Pectobacterium carotovorum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-22 Released: 2025-04-23 
• Deposition Author(s): Wojnowska, M., Bogucka, A.
• Funding Organization(s): University of Cambridge

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.205 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Models: experimental

Literature

Receptor-substrate competition for the TonB homologue FusB suggests a model for ferredoxin import in Pectobacterium spp

Wojnowska, M., Flores, V., Yelland, T., Fisher, S.R., Bogucka, A., Stott, K., Walker, D.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.10.16.682781

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.66 kDa 
• Atom Count: 1,777 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein TonB,Ferredoxin-1, chloroplastic	A	198	Pectobacterium carotovorum	Mutation(s): 0  Gene Names: ECA0877, PETF
UniProt
Find proteins for P00221 (Spinacia oleracea) Explore P00221  Go to UniProtKB:  P00221
Find proteins for Q6D8U5 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D8U5  Go to UniProtKB:  Q6D8U5
UniProt Groups	Q6D8U5P00221

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.205 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.678	α = 90
b = 67.446	β = 90
c = 85.969	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Wojnowska, M., Bogucka, A.

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Funding Organization	Location	Grant Number
University of Cambridge	United Kingdom	--

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 1.1: 2025-11-05
  Changes: Database references