7ME3

YfeA oligomer crystal 3, form 2

• PDB DOI: https://doi.org/10.2210/pdb7ME3/pdb

• Classification: METAL TRANSPORT
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-04-06 Released: 2021-08-25 
• Deposition Author(s): Radka, C.D., Aller, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.218 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Literature

Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site

Radka, C.D., Aller, S.G.

(2021) Acta Crystallogr F Struct Biol Commun 77: 286-293

• DOI: https://doi.org/10.1107/S2053230X21008086

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.57 kDa 
• Atom Count: 4,660 
• Modelled Residue Count: 554 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic chelated iron-binding protein YfeA	A, B	323	Yersinia pestis	Mutation(s): 0  Gene Names: yfeA, YPO2439, y1897, YP_2227
UniProt
Find proteins for Q56952 (Yersinia pestis) Explore Q56952  Go to UniProtKB:  Q56952

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], H [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	D [auth A], G [auth B], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.218 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.09	α = 90
b = 75.85	β = 90
c = 106.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Radka, C.D., Aller, S.G.

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 1.1: 2021-09-08
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description