4A1R | pdb_00004a1r

The Structure of Serratia marcescens Lip, a membrane bound component of the Type VI Secretion System.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.292 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

The Structure of Serratia Marcescens Lip, a Membrane-Bound Component of the Type Vi Secretion System

Rao, V.A.Shepherd, S.M.English, G.Coulthurst, S.J.Hunter, W.N.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1065

  • DOI: https://doi.org/10.1107/S0907444911046300
  • Primary Citation Related Structures: 
    4A1R

  • PubMed Abstract: 

    Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29-176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein-protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners.


  • Organizational Affiliation
    • College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.

Macromolecule Content 

  • Total Structure Weight: 65.45 kDa 
  • Atom Count: 4,787 
  • Modeled Residue Count: 558 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LIP
A, B, C, D
149Serratia marcescensMutation(s): 0 
UniProt
Find proteins for G5EA77 (Serratia marcescens)
Explore G5EA77 
Go to UniProtKB:  G5EA77
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5EA77
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.292 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.73α = 90
b = 77.75β = 98.31
c = 54.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references
  • Version 1.2: 2012-02-29
    Changes: Other
  • Version 1.3: 2013-03-20
    Changes: Derived calculations
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description