9HRJ | pdb_00009hrj

Structure of YIUA from Yersinia ruckeri

• PDB DOI: https://doi.org/10.2210/pdb9HRJ/pdb

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


• Deposited: 2024-12-18 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: 
  0.310 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structure of YIUA from Yersinia ruckeri

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.

Macromolecule Content 

• Total Structure Weight: 76.54 kDa 
• Atom Count: 5,422 
• Modeled Residue Count: 671 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic substrate-binding transport protein	A, B	349	Yersinia ruckeri	Mutation(s): 0  Gene Names: CSF007_11785
UniProt
Find proteins for A0A085U4N5 (Yersinia ruckeri) Explore A0A085U4N5  Go to UniProtKB:  A0A085U4N5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.310 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Diffraction Data: https://doi.org/10.15124/bb372531-5f97-499f-a540-313ac38a568a

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.598	α = 90
b = 68.474	β = 96.75
c = 112.908	γ = 90

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