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Crystal structure of the N-terminal domain of the Legionella pneumophila protein SidC at 2.4A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of the N-terminal domain of the Legionella protein SidC

Gazdag, E.M.Schobel, S.Shkumatov, A.V.Goody, R.S.Itzen, A.

(2014) J.Struct.Biol. 186: 188-194

  • DOI: 10.1016/j.jsb.2014.02.003

  • PubMed Abstract: 
  • The Gram-negative bacterium Legionella pneumophila is the causative agent of Legionnaires' disease. During infection of eukaryotic cells, the bacterium releases about 300 different bacterial effector molecules that aid in the establishment of the Leg ...

    The Gram-negative bacterium Legionella pneumophila is the causative agent of Legionnaires' disease. During infection of eukaryotic cells, the bacterium releases about 300 different bacterial effector molecules that aid in the establishment of the Legionella-containing vacuole (LCV) among which SidC is one of these secreted proteins. However, apart from membrane lipid binding the function of SidC remains elusive. In order to characterize SidC further, we have determined the crystal structure of the N-terminal domain of SidC (amino acids 1-609, referred to as SidC-N) at 2.4Å resolution. SidC-N reveals a novel fold in which 4 potential subdomains (A-D) are arranged in a crescent-like structure. None of these subdomains currently has any known structural homologues, raising the question of how this fold has evolved. These domains are highly interconnected, with a low degree of flexibility towards each other. Due to the extended arrangement of the subdomains, SidC-N may contain multiple binding sites for potential interaction partners.


    Organizational Affiliation

    Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49, 3000 Leuven, Belgium.,Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, Dortmund 44227, Germany.,Center for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany. Electronic address: aymelt.itzen@tum.de.,Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, Dortmund 44227, Germany. Electronic address: roger.goody@mpi-dortmund.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SidC, interaptin
A, B, C, D
611Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 0 
Gene Names: sidC
Find proteins for Q5ZSK6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZSK6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 119.055α = 90.00
b = 119.055β = 90.00
c = 201.700γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references