6ZHP

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic

• PDB DOI: https://doi.org/10.2210/pdb6ZHP/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2020-06-23 Released: 2021-05-05 
• Deposition Author(s): Sousa, C.F., Morais-Cabral, J., Gameiro, P.
• Funding Organization(s): Foundation for Science and Technology (FCT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic

Sousa, C.F., Morais-Cabral, J., Gameiro, P.

To be published.

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: 39.94 kDa 
• Atom Count: 2,836 
• Modelled Residue Count: 341 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin F	A [auth B]	362	Escherichia coli K-12	Mutation(s): 0  Gene Names: ompF, cmlB, coa, cry, tolF, b0929, JW0912 Membrane Entity: Yes
UniProt
Find proteins for P02931 (Escherichia coli (strain K12)) Explore P02931  Go to UniProtKB:  P02931

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QLB	C [auth B], D [auth B]	2-[2-(2-octoxyethoxy)ethoxy]ethanol C14 H30 O4 XIVLVYLYOMHUGB-UHFFFAOYSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.943	α = 90
b = 135.943	β = 90
c = 51.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Sousa, C.F., Morais-Cabral, J., Gameiro, P.

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Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	--

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description