5KBN | pdb_00005kbn

The crystal structure of fluoride channel Fluc Ec2 F80I Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Mechanistic signs of double-barreled structure in a fluoride ion channel.

Last, N.B.Kolmakova-Partensky, L.Shane, T.Miller, C.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.18767
  • Primary Citation Related Structures: 
    5KBN, 5KOM

  • PubMed Abstract: 

    The Fluc family of F(-) ion channels protects prokaryotes and lower eukaryotes from the toxicity of environmental F(-). In bacteria, these channels are built as dual-topology dimers whereby the two subunits assemble in antiparallel transmembrane orientation. Recent crystal structures suggested that Fluc channels contain two separate ion-conduction pathways, each with two F(-) binding sites, but no functional correlates of this unusual architecture have been reported. Experiments here fill this gap by examining the consequences of mutating two conserved F(-)-coordinating phenylalanine residues. Substitution of each phenylalanine specifically extinguishes its associated F(-) binding site in crystal structures and concomitantly inhibits F(-) permeation. Functional analysis of concatemeric channels, which permit mutagenic manipulation of individual pores, show that each pore can be separately inactivated without blocking F(-) conduction through its symmetry-related twin. The results strongly support dual-pathway architecture of Fluc channels.


  • Organizational Affiliation
    • Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States.

Macromolecule Content 

  • Total Structure Weight: 54.84 kDa 
  • Atom Count: 3,560 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 488 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative fluoride ion transporter CrcB
A, B
147Escherichia coliMutation(s): 2 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for Q6J5N4 (Escherichia coli)
Explore Q6J5N4 
Go to UniProtKB:  Q6J5N4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6J5N4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
monobody
C, D
97Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMU

Query on DMU



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
J [auth B],
L [auth C]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
F

Query on F



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B]
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.655α = 90
b = 87.655β = 90
c = 143.625γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1-GM107023

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description