3FYX

The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

On the function and structure of synthetically modified porins.

Reitz, S.Cebi, M.Reiss, P.Studnik, G.Linne, U.Koert, U.Essen, L.O.

(2009) Angew.Chem.Int.Ed.Engl. 48: 4853-4857

  • DOI: 10.1002/anie.200900457

  • PubMed Abstract: 
  • The attachment of modulators to a trimeric porin ion channel was investigated (see picture of the trimer with a crown ether modulator (orange)). The interplay of modulator and protein is essential for the conformational heterogeneity of the hybrid ch ...

    The attachment of modulators to a trimeric porin ion channel was investigated (see picture of the trimer with a crown ether modulator (orange)). The interplay of modulator and protein is essential for the conformational heterogeneity of the hybrid channel. Single-site attachment in large pores is not sufficient to change the electrophysiological characteristics of the pores-such change requires additional noncovalent interactions or second-site attachments.


    Organizational Affiliation

    Fachbereich Chemie, Philipps-Universit├Ąt Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein F
A
340Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ompF (cmlB, coa, cry, tolF)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpF Porin
Find proteins for P02931 (Escherichia coli (strain K12))
Go to UniProtKB:  P02931
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
451
Query on 451

Download SDF File 
Download CCD File 
A
N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide
N-(Dibenzo-18-crown-6-ether)-acetamide
C22 H27 N O7
YHKGWOJTUMJPNW-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.520α = 90.00
b = 135.520β = 90.00
c = 47.520γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance