3FYX

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

• PDB DOI: https://doi.org/10.2210/pdb3FYX/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2009-01-23 Released: 2009-06-30 
• Deposition Author(s): Reitz, S., Cebi, M., Koert, U., Essen, L.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.249 
• R-Value Observed: 0.252 

Starting Model: experimental

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

• PubMed: 19322865 
• DOI: https://doi.org/10.1002/anie.200900457
• Primary Citation of Related Structures:  
  3FYX


• 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 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.

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Organizational Affiliation: 

Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.74 kDa 
• Atom Count: 2,669 
• Modelled Residue Count: 340 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein F	A	340	Escherichia coli K-12	Mutation(s): 1  Gene Names: b0929, cmlB, coa, cry, JW0912, ompF, tolF Membrane Entity: Yes
UniProt
Find proteins for P02931 (Escherichia coli (strain K12)) Explore P02931  Go to UniProtKB:  P02931

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
451	B [auth A]	N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide C22 H27 N O7 YHKGWOJTUMJPNW-UHFFFAOYSA-N
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.249 
• R-Value Observed: 0.252 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.52	α = 90
b = 135.52	β = 90
c = 47.52	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Reitz, S., Cebi, M., Koert, U., Essen, L.O.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary