3SVI | pdb_00003svi

Structure of the Pto-binding domain of HopPmaL generated by limited thermolysin digestion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.218 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3SVI

This is version 1.5 of the entry. See complete history

Literature

Structural Analysis of HopPmaL Reveals the Presence of a Second Adaptor Domain Common to the HopAB Family of Pseudomonas syringae Type III Effectors.

Singer, A.U.Wu, B.Yee, A.Houliston, S.Xu, X.Cui, H.Skarina, T.Garcia, M.Semesi, A.Arrowsmith, C.H.Savchenko, A.

(2012) Biochemistry 51: 1-3

  • DOI: https://doi.org/10.1021/bi2013883
  • Primary Citation Related Structures: 
    2LF3, 2LF6, 3SVI, 3TJY

  • PubMed Abstract: 

    HopPmaL is a member of the HopAB family of type III effectors present in the phytopathogen Pseudomonas syringae. Using both X-ray crystallography and solution nuclear magnetic resonance, we demonstrate that HopPmaL contains two structurally homologous yet functionally distinct domains. The N-terminal domain corresponds to the previously described Pto-binding domain, while the previously uncharacterised C-terminal domain spans residues 308-385. While structurally similar, these domains do not share significant sequence similarity and most importantly demonstrate significant differences in key residues involved in host protein recognition, suggesting that each of them targets a different host protein.


  • Organizational Affiliation
    • Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada.

Macromolecule Content 

  • Total Structure Weight: 9.94 kDa 
  • Atom Count: 759 
  • Modeled Residue Count: 79 
  • Deposited Residue Count: 83 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type III effector HopAB283Pseudomonas syringae pv. maculicola str. ES4326Mutation(s): 0 
Gene Names: HopPmaLPMA4326_19338

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.218 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.277α = 90
b = 57.277β = 90
c = 55.658γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXCDphasing
SHELXEmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references
  • Version 1.2: 2012-01-25
    Changes: Database references
  • Version 1.3: 2012-02-29
    Changes: Structure summary
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary