6ZHP | pdb_00006zhp

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 PDBTM MemProtMD

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.207 (Depositor), 0.212 (DCC)
R-Value Work:
0.179 (Depositor)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic

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

To be published.

Macromolecule Content

Total Structure Weight: 39.94 kDa
Atom Count: 2,836
Modeled Residue Count: 341
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QLB Query on QLB Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	2-[2-(2-octoxyethoxy)ethoxy]ethanol C₁₄ H₃₀ O₄ XIVLVYLYOMHUGB-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.207 (Depositor), 0.212 (DCC)
R-Value Work: 0.179 (Depositor)
R-Value Observed: 0.180 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-05

Deposition Author(s):

Morais-Cabral, J.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.