3F4I

Crystal Structure of LeuT bound to L-selenomethionine and sodium

• PDB DOI: https://doi.org/10.2210/pdb3F4I/pdb

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


• Deposited: 2008-10-31 Released: 2008-12-23 
• Deposition Author(s): Singh, S.K., Piscitelli, C.L., Yamashita, A., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.218 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.78 kDa 
• Atom Count: 4,267 
• Modelled Residue Count: 509 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter	A	519	Aquifex aeolicus	Mutation(s): 0  Gene Names: snf, aq_2077 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
BOG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
MSE	B [auth A]	SELENOMETHIONINE C5 H11 N O2 Se RJFAYQIBOAGBLC-BYPYZUCNSA-N
NA	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.218 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.777	α = 90
b = 86.703	β = 95.85
c = 81.692	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Singh, S.K., Piscitelli, C.L., Yamashita, A., Gouaux, E.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2023-11-15
  Changes: Data collection