6JDP

the imm52 family protein TsiT (PA3908) from Pseudomonas aeruginosa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural characterization of the Imm52 family protein TsiT in Pseudomonas aeruginosa.

She, Z., Geng, Z., Xu, J.H., Li, Y.H., Dong, Y.H.

(2019) Protein Sci 28: 971-975

  • DOI: 10.1002/pro.3597
  • Primary Citation of Related Structures:  
    6JDP

  • PubMed Abstract: 

    • The bacterial type VI secretion system (T6SS) utilizes many toxic effectors to gain advantage over interbacterial competition and eukaryotic host infection. Meanwhile, the cognate immunity proteins of these effectors are employed to protect themselves from the virulence ...

    The bacterial type VI secretion system (T6SS) utilizes many toxic effectors to gain advantage over interbacterial competition and eukaryotic host infection. Meanwhile, the cognate immunity proteins of these effectors are employed to protect themselves from the virulence. TseT and TsiT form an effector-immunity (E-I) protein pair secreted by T6SS of Pseudomonas aeruginosa. TseT is toxic for other bacteria, whereas TsiT can suppress the virulence of TseT. Here, we report the crystal structure of TsiT at 1.6 Å resolution. TsiT is a typical α + β class protein and belongs to a novel Imm52 protein family of the polymorphic toxin system. Apart from TsiT, only one structure of the Imm52 family proteins is present in the Protein Data Bank (PDB), but that structure is not characterized and shares low sequence identity with TsiT. We characterized the basic features of TsiT structure and identified conserved residues of the Imm52 family proteins according to homology comparison. Our work provided structural information of a new protein family and should aid future functional studies.

    Organizational Affiliation: 

    Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Imm52 family proteinA262Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA3908
UniProt
Find proteins for Q9HXA5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HXA5 
Go to UniProtKB:  Q9HXA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HXA5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.96α = 90
b = 86.96β = 90
c = 81.108γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-02 
  • Released Date: 2019-03-20 
    • Deposition Author(s): She, Z.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31700651

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references