9HT5 | pdb_00009ht5

Structure of YIUA from Yersinia ruckeri with Iron and nitrilotriacetic acid

• PDB DOI: https://doi.org/10.2210/pdb9HT5/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Yersinia ruckeri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-19 Released: 2025-11-12 
• Deposition Author(s): Thompson, S., Thomsen, E., Duhme-Klair, A., Butler, A., Grogan, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.253 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of YIUA from Yersinia ruckeri with Iron and nitrilotriacetic acid

Thompson, S., Thomsen, E., Duhme-Klair, A., Butler, A., Grogan, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 114.86 kDa 
• Atom Count: 7,790 
• Modeled Residue Count: 1,001 
• Deposited Residue Count: 1,041 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic substrate-binding transport protein	A, B, C	347	Yersinia ruckeri	Mutation(s): 0  Gene Names: CSF007_11785
UniProt
Find proteins for A0A085U4N5 (Yersinia ruckeri) Explore A0A085U4N5  Go to UniProtKB:  A0A085U4N5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NTA (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	NITRILOTRIACETIC ACID C6 H9 N O6 MGFYIUFZLHCRTH-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.253 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.146	α = 101.36
b = 59.386	β = 94.49
c = 101.171	γ = 100.54

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Thompson, S., Thomsen, E., Duhme-Klair, A., Butler, A., Grogan, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release