5IV9

The LPS Transporter LptDE from Klebsiella pneumoniae, full-length


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.37 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.303 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.

Botos, I.Majdalani, N.Mayclin, S.J.McCarthy, J.G.Lundquist, K.Wojtowicz, D.Barnard, T.J.Gumbart, J.C.Buchanan, S.K.

(2016) Structure 24: 965-976

  • DOI: https://doi.org/10.1016/j.str.2016.03.026
  • Primary Citation of Related Structures:  
    5IV8, 5IV9, 5IVA, 5IXM

  • PubMed Abstract: 

    Incorporation of lipopolysaccharide (LPS) into the outer membrane of Gram-negative bacteria is essential for viability, and is accomplished by a two-protein complex called LptDE. We solved crystal structures of the core LptDE complexes from Yersinia pestis, Klebsiella pneumoniae, Pseudomonas aeruginosa, and a full-length structure of the K. pneumoniae LptDE complex. Our structures adopt the same plug and 26-strand β-barrel architecture found recently for the Shigella flexneri and Salmonella typhimurium LptDE structures, illustrating a conserved fold across the family. A comparison of the only two full-length structures, SfLptDE and our KpLptDE, reveals a 21° rotation of the LptD N-terminal domain that may impart flexibility on the trans-envelope LptCAD scaffold. Utilizing mutagenesis coupled to an in vivo functional assay and molecular dynamics simulations, we demonstrate the critical role of Pro231 and Pro246 in the function of the LptD lateral gate that allows partitioning of LPS into the outer membrane.


  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly protein LptD758Klebsiella pneumoniaeMutation(s): 0 
Gene Names: implptD
Membrane Entity: Yes 
UniProt
Find proteins for C4T9I0 (Klebsiella pneumoniae)
Explore C4T9I0 
Go to UniProtKB:  C4T9I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4T9I0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptE177Klebsiella pneumoniaeMutation(s): 0 
Gene Names: lptEAPU20_03225
Membrane Entity: Yes 
UniProt
Find proteins for A0A0J4W1Y0 (Klebsiella variicola)
Explore A0A0J4W1Y0 
Go to UniProtKB:  A0A0J4W1Y0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J4W1Y0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.37 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.303 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.219α = 90
b = 155.459β = 90
c = 197.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-15
    Changes: Database references