8FT5 | pdb_00008ft5

Crystal structure of LeuT soaked with Crown-5

• PDB DOI: https://doi.org/10.2210/pdb8FT5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-01-11 Released: 2023-11-22 
• Deposition Author(s): Karasawa, A., Liu, H., Quick, M., Hendrickson, A.H., Liu, Q.
• 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: 3.80 Å
• R-Value Free: 
  0.313 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.271 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Starting Model: experimental

Literature

Crystallographic characterization of sodium ions in a bacterial leucine/sodium symporter

Karasawa, A., Liu, H., Quick, M., Hendrickson, W.A., Liu, Q.

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: 58.53 kDa 
• Atom Count: 4,045 
• Modeled Residue Count: 507 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+):neurotransmitter symporter (Snf family)	A	520	Aquifex aeolicus	Mutation(s): 0  Gene Names: snf Membrane Entity: Yes
UniProt
Find proteins for O67854 (Aquifex aeolicus (strain VF5)) Explore O67854  Go to UniProtKB:  O67854

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEU (Subject of Investigation/LOI)	E [auth A]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.313 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.271 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.442	α = 90
b = 87.383	β = 95.062
c = 80.798	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Karasawa, A., Liu, H., Quick, M., Hendrickson, A.H., Liu, Q.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116799

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release