6ENE

OmpF orthologue from Enterobacter cloacae (OmpE35)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins.

Acosta-Gutierrez, S.Ferrara, L.Pathania, M.Masi, M.Wang, J.Bodrenko, I.Zahn, M.Winterhalter, M.Stavenger, R.A.Pages, J.M.Naismith, J.H.van den Berg, B.Page, M.G.P.Ceccarelli, M.

(2018) Acs Infect Dis. 4: 1487-1498

  • DOI: 10.1021/acsinfecdis.8b00108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small, hydrophilic molecules, including most important antibiotics in clinical use, cross the Gram-negative outer membrane through the water-filled channels provided by porins. We have determined the X-ray crystal structures of the principal general ...

    Small, hydrophilic molecules, including most important antibiotics in clinical use, cross the Gram-negative outer membrane through the water-filled channels provided by porins. We have determined the X-ray crystal structures of the principal general porins from three species of Enterobacteriaceae, namely Enterobacter aerogenes, Enterobacter cloacae, and Klebsiella pneumoniae, and determined their antibiotic permeabilities as well as those of the orthologues from Escherichia coli. Starting from the structure of the porins and molecules, we propose a physical mechanism underlying transport and condense it in a computationally efficient scoring function. The scoring function shows good agreement with in vitro penetration data and will enable the screening of virtual databases to identify molecules with optimal permeability through porins and help to guide the optimization of antibiotics with poor permeation.


    Organizational Affiliation

    Division of Structural Biology , Nuffield Department of Medicine , Roosevelt Drive , Oxford OX3 7BN , United Kingdom.,Research Complex at Harwell , Rutherford Laboratory , Didcot , OX11 0FA , United Kingdom.,UMR_MD1 Inserm U1261, Membranes et Cibles Thérapeutiques , Aix-Marseille Université, Facultés de Pharmacie et de Médecine , 27 Bd Jean Moulin , 13005 Marseille , France.,Department of Life Sciences and Chemistry , Jacobs University Bremen , 28719 Bremen , Germany.,Department of Physics , University of Cagliari, Cittadella Universitaria di Monserrato , SP Monserrato-Sestu Km 0.8 , Monserrato , 09042 , Italy.,Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne NE2 4HH , United Kingdom.,Antibacterial DPU , GlaxoSmithKline , 1250 Collegeville Road , Collegeville , Pennsylvania 19426 , United States.,Biomedical Sciences Research Complex , University of St Andrews , St Andrews KY16 9RH , United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein (Porin)
A, B, C
329Enterobacter cloacaeMutation(s): 0 
Gene Names: ompF
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpE35 (OmpF)
Find proteins for A0A0M7H8A9 (Enterobacter cloacae)
Go to UniProtKB:  A0A0M7H8A9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
C8E
Query on C8E

Download SDF File 
Download CCD File 
A, C
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 137.548α = 90.00
b = 187.253β = 90.00
c = 122.957γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union 7th Framework ProgrammeUnited Kingdom115525

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-11-13
    Type: Data collection, Database references