4A0E

Crystal structure of the cytoplasmic N-terminal domain of Yersinia pestis YscD

• PDB DOI: https://doi.org/10.2210/pdb4A0E/pdb

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


• Deposited: 2011-09-08 Released: 2012-02-29 
• Deposition Author(s): Lountos, G.T., Tropea, J.E., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.256 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Structure of the Cytoplasmic Domain of Yersinia Pestis Yscd, an Essential Component of the Type III Secretion System

Lountos, G.T., Tropea, J.E., Waugh, D.S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 201

• PubMed: 22349221 
• DOI: https://doi.org/10.1107/S0907444911054308
• Primary Citation of Related Structures:  
  4A0E


• PubMed Abstract: 
  

  The Yersinia pestis YscD protein is an essential component of the type III secretion system. YscD consists of an N-terminal cytoplasmic domain (residues 1-121), a transmembrane linker (122-142) and a large periplasmic domain (143-419). Both the cytoplasmic and the periplasmic domains are required for the assembly of the type III secretion system. Here, the structure of the YscD cytoplasmic domain solved by SAD phasing is presented. Although the three-dimensional structure is similar to those of forkhead-associated (FHA) domains, comparison with the structures of canonical FHA domains revealed that the cytoplasmic domain of YscD lacks the conserved residues that are required for binding phosphothreonine and is therefore unlikely to function as a true FHA domain.

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Organizational Affiliation: 

Basic Science Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.

Biological Assembly 1  

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

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

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: 26.97 kDa 
• Atom Count: 1,738 
• Modelled Residue Count: 216 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE III SECRETION PROTEIN	A, B	123	Yersinia pestis	Mutation(s): 0
UniProt
Find proteins for Q56975 (Yersinia pestis) Explore Q56975  Go to UniProtKB:  Q56975

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.256 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.227	α = 90
b = 118.227	β = 90
c = 118.227	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Lountos, G.T., Tropea, J.E., Waugh, D.S.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Other