Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.49 kDa 
• Atom Count: 2312 
• Residue Count: 274 
• Unique protein chains: 1

6Q1D

Holo YfeA reconstituted by zinc soaking

• DOI: 10.2210/pdb6Q1D/pdb

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


• Deposited: 2019-08-03 Released: 2019-09-04 
• Deposition Author(s): Radka, C.D., Labiuk, S.L., DeLucas, L.J., Aller, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.219 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms.

Radka, C.D., Labiuk, S.L., DeLucas, L.J., Aller, S.G.

(2019) Acta Crystallogr D Struct Biol 75: 831-840

• PubMed: 31478906 
• DOI: 10.1107/S2059798319010866
• Structures With Same Primary Citation


• PubMed Abstract: 
  

In the structural biology of bacterial substrate-binding proteins (SBPs), a growing number of comparisons between substrate-bound and substrate-free forms of metal atom-binding (cluster A-I) SBPs have revealed minimal structural differences between forms. These observations contrast with SBPs that bind substrates such as amino acids or nucleic acids and may undergo >60° rigid-body rotations. Substrate transfer in these SBPs is described by a Venus flytrap model, although this model may not apply to all SBPs. In this report, structures are presented of substrate-free (apo) and reconstituted substrate-bound (holo) YfeA, a polyspecific cluster A-I SBP from Yersinia pestis. It is demonstrated that an apo cluster A-I SBP can be purified by fractionation when co-expressed with its cognate transporter, adding an alternative strategy to the mutagenesis or biochemical treatment used to generate other apo cluster A-I SBPs. The apo YfeA structure contains 111 disordered protein atoms in a mobile helix located in the flexible carboxy-terminal lobe. Metal binding triggers a 15-fold reduction in the solvent-accessible surface area of the metal-binding site and reordering of the 111 protein atoms in the mobile helix. The flexible lobe undergoes a 13.6° rigid-body rotation that is driven by a spring-hammer metal-binding mechanism. This asymmetric rigid-body rotation may be unique to metal atom-binding SBPs (i.e. clusters A-I, A-II and D-IV).

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Organizational Affiliation: 

Department of Pharmacology and Toxicology, Birmingham, AL 35294, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Periplasmic chelated iron-binding protein YfeA	A	311	Yersinia pestis	Mutation(s): 0  Gene Names: yfeA, YPO2439, y1897, YP_2227
Find proteins for Q56952 (Yersinia pestis) Go to UniProtKB:  Q56952

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.219 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.864	α = 90
b = 50.922	β = 90
c = 115.536	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

• Deposited Date: 2019-08-03 
• Released Date: 2019-09-04 
Deposition Author(s): Radka, C.D., Labiuk, S.L., DeLucas, L.J., Aller, S.G.

Revision History 

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references
• Version 1.2: 2019-09-25
  Changes: Data collection, Database references