4OOJ

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: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.jsb.2014.02.003
  • Primary Citation of Related Structures:  
    4OOJ

  • 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 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

    Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, Dortmund 44227, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SidC, interaptin
A, B, C, D
611Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: sidC
UniProt
Find proteins for Q5ZSK6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZSK6 
Go to UniProtKB:  Q5ZSK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZSK6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth C],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.055α = 90
b = 119.055β = 90
c = 201.7γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description