3PGS | pdb_00003pgs

Phe3Gly mutant of EcFadL

PDB DOI: https://doi.org/10.2210/pdb3PGS/pdb

Classification: LIPID TRANSPORT
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2010-11-02 Released: 2011-05-25
Deposition Author(s): van den Berg, B., Lepore, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.192 (Depositor), 0.181 (DCC)
R-Value Work:
0.167 (Depositor), 0.160 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

From the Cover: Ligand-gated diffusion across the bacterial outer membrane.

Lepore, B.W., Indic, M., Pham, H., Hearn, E.M., Patel, D.R., van den Berg, B.

(2011) Proc Natl Acad Sci U S A 108: 10121-10126

PubMed: 21593406 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1018532108
Primary Citation Related Structures:
2R89, 2R8A, 3PF1, 3PGR, 3PGS, 3PGU

PubMed Abstract:
Ligand-gated channels, in which a substrate transport pathway is formed as a result of the binding of a small-molecule chemical messenger, constitute a diverse class of membrane proteins with important functions in prokaryotic and eukaryotic organisms. Despite their widespread nature, no ligand-gated channels have yet been found within the outer membrane (OM) of Gram-negative bacteria. Here we show, using in vivo transport assays, intrinsic tryptophan fluorescence and X-ray crystallography, that high-affinity (submicromolar) substrate binding to the OM long-chain fatty acid transporter FadL from Escherichia coli causes conformational changes in the N terminus that open up a channel for substrate diffusion. The OM long-chain fatty acid transporter FadL from E. coli is a unique paradigm for OM diffusion-driven transport, in which ligand gating within a β-barrel membrane protein is a prerequisite for channel formation.

Organizational Affiliation

University of Massachusetts Medical School, Program in Molecular Medicine, 373 Plantation Street, Worcester, MA 01605, USA.

Macromolecule Content

Total Structure Weight: 99.97 kDa
Atom Count: 8,014
Modeled Residue Count: 853
Deposited Residue Count: 854
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-chain fatty acid transport protein	A, B	427	Escherichia coli K-12	Mutation(s): 1 Gene Names: b2344, fadL, JW2341, ttr Membrane Entity: Yes
UniProt
Find proteins for P10384 (Escherichia coli (strain K12)) Explore P10384 Go to UniProtKB: P10384
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10384
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
C8E Query on C8E Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain E [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain N [auth A] SDF format, chain D [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain N [auth A] MOL2 format, chain D [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain N [auth A] mmCIF format, chain D [auth A]	AA [auth B] D [auth A] E [auth A] M [auth A] N [auth A] AA [auth B], D [auth A], E [auth A], M [auth A], N [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], V [auth B], W [auth B], X [auth B], Z [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Z [auth B]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	O [auth A], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain Y [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.192 (Depositor), 0.181 (DCC)
R-Value Work: 0.167 (Depositor), 0.160 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.068	α = 90
b = 147.513	β = 90
c = 151.092	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

van den Berg, B.

Lepore, B.W.

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description