9IF3 | pdb_00009if3

Structure of YIUA from Yersinia ruckeri with Iron and DHB-L-Arg-L-Ser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.277 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Yersinia ruckeri YRB periplasmic binding protein YiuA selectively recognizes a Fe(III)-mono-catecholate siderophore.

Thomsen, E.Thompson, S.Stow, P.R.Cukor, M.Grogan, G.Duhme-Klair, A.K.Butler, A.

(2025) Chem Commun (Camb) 61: 17653-17656

  • DOI: https://doi.org/10.1039/d5cc05103g
  • Primary Citation of Related Structures:  
    9HRP, 9IF3

  • PubMed Abstract: 

    The marine pathogen Yersinia ruckeri synthesizes the tri-catecholate siderophore ruckerbactin, Rb, (DHB- L Arg- L Ser) 3 , to acquire iron during infection. Its biosynthetic gene cluster encodes a single periplasmic binding protein, RupB, which surprisingly does not bind Fe(III)-Rb nor the Fe(III) complexes of its hydrolysis products, the di- and mono-catecholate siderophores Rb DC and Rb MC , with biologically relevant affinities. Instead, the periplasmic binding protein YiuA, encoded in a different region of the chromosome, binds the 1 : 2 Fe(III) complex of the mono-catecholate Rb MC , Fe(III)-(Rb MC ) 2 . YiuA is the first periplasmic binding protein (PBP) to selectively recognize a mono-catecholate siderophore, the structural basis of which was illuminated through X-ray crystallography of YiuA bound to Fe(III)-(Rb MC ) 2 .


  • Organizational Affiliation
    • University of California, Department of Chemistry & Biochemistry, Santa Barbara, CA 93106-9510, USA. butler@chem.ucsb.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic substrate-binding transport protein
A, B, C, D, E
A, B, C, D, E, F, G, H
349Yersinia ruckeriMutation(s): 0 
Gene Names: CSF007_11785
UniProt
Find proteins for A0A085U4N5 (Yersinia ruckeri)
Explore A0A085U4N5 
Go to UniProtKB:  A0A085U4N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A085U4N5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I15 (Subject of Investigation/LOI)
Query on A1I15

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
FA [auth E]
J [auth A]
JA [auth F]
AA [auth D],
EA [auth E],
FA [auth E],
J [auth A],
JA [auth F],
K [auth A],
KA [auth F],
O [auth B],
OA [auth G],
P [auth B],
PA [auth G],
S [auth C],
T [auth C],
VA [auth H],
WA [auth H],
Z [auth D]
(2~{S})-2-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-5-carbamimidamido-pentanoyl]amino]-3-oxidanyl-propanoic acid
C16 H23 N5 O7
LXNCWECCTQQXPQ-UWVGGRQHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
GA [auth E]
HA [auth E]
L [auth A]
BA [auth D],
CA [auth D],
GA [auth E],
HA [auth E],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
Q [auth B],
QA [auth G],
RA [auth G],
SA [auth G],
TA [auth G],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
XA [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
DA [auth E]
I [auth A]
IA [auth F]
N [auth B]
NA [auth G]
DA [auth E],
I [auth A],
IA [auth F],
N [auth B],
NA [auth G],
R [auth C],
UA [auth H],
Y [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.277 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.073α = 90
b = 80.018β = 89.86
c = 223.696γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references
  • Version 1.2: 2025-11-19
    Changes: Database references