6ENE

OmpF orthologue from Enterobacter cloacae (OmpE35)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acsinfecdis.8b00108
  • Primary Citation of Related Structures:  
    5O77, 5O79, 6ENE

  • 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 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

    Department of Physics , University of Cagliari, Cittadella Universitaria di Monserrato , SP Monserrato-Sestu Km 0.8 , Monserrato , 09042 , Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein (Porin)
A, B, C
329Enterobacter cloacaeMutation(s): 0 
Gene Names: ompFNCTC10005_05711
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M7H8A9 (Enterobacter cloacae)
Explore A0A0M7H8A9 
Go to UniProtKB:  A0A0M7H8A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M7H8A9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth C]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
F [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
L [auth B]
M [auth B]
N [auth C]
D [auth A],
E [auth A],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.548α = 90
b = 187.253β = 90
c = 122.957γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union 7th Framework ProgrammeUnited Kingdom115525

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary