8FQ9

Crystal structure of a ligand-bound cation-site mutant D55C of a melibiose transporter

• PDB DOI: https://doi.org/10.2210/pdb8FQ9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-01-05 Released: 2024-06-05 
• Deposition Author(s): Guan, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.288 
• R-Value Work: 0.263 
• R-Value Observed: 0.266 

Starting Model: experimental

Literature

Crystal structure of a ligand-bound cation-site mutant D55C of a melibiose transporter

Guan, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 54.84 kDa 
• Atom Count: 3,616 
• Modelled Residue Count: 455 
• Deposited Residue Count: 485 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melibiose permease	A	485	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1  Gene Names: melB, STM4299 Membrane Entity: Yes
UniProt
Find proteins for P30878 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P30878  Go to UniProtKB:  P30878

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMO (Subject of Investigation/LOI)	C [auth A]	dodecyl 6-O-alpha-D-galactopyranosyl-beta-D-glucopyranoside C24 H46 O11 HBVAWIPMNSJELA-RWNQQKCBSA-N
1PE (Subject of Investigation/LOI)	B [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002459 (LMO)	C [auth A]	Dodecyl melibioside	Polysaccharide / Protein binding

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.288 
• R-Value Work: 0.263 
• R-Value Observed: 0.266 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.225	α = 90
b = 127.225	β = 90
c = 104.042	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Guan, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM122759

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release