3B29

Human leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside

• PDB DOI: https://doi.org/10.2210/pdb3B29/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Schizosaccharomyces pombe
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2011-07-22 Released: 2011-12-14 
• Deposition Author(s): Saino, H., Ago, H., Miyano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.209 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

Seleno-detergent MAD phasing of leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside

Saino, H., Ago, H., Ukita, Y., Miyano, M.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1666-1673

• PubMed: 22139193 
• DOI: https://doi.org/10.1107/S1744309111042345
• Primary Citation of Related Structures:  
  3B29


• PubMed Abstract: 
  

  Dodecyl-β-D-selenomaltoside (SeDDM) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-D-maltoside. Seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography. Crystals of a nuclear membrane-embedded enzyme, leukotriene C(4) synthase (LTC(4)S), in complex with SeDDM were prepared and a multiwavelength anomalous diffraction (MAD) experiment was performed. The SeDDM in the LTC(4)S crystal exhibited sufficient anomalous diffraction for determination of the structure using MAD phasing.

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Organizational Affiliation: 

Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.68 kDa 
• Atom Count: 1,187 
• Modelled Residue Count: 142 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene C4 synthase	A	156	Homo sapiens	Mutation(s): 0  Gene Names: LTC4S EC: 4.4.1.20 (PDB Primary Data), 2.5.1 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens) Explore Q16873  Go to UniProtKB:  Q16873
PHAROS:  Q16873

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LSM	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	dodecyl 4-O-alpha-D-glucopyranosyl-1-seleno-beta-D-glucopyranoside C24 H46 O10 Se MEIBWTYMLPEGMV-ALYNCGSASA-N
GSH	B [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.209 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.594	α = 90
b = 168.594	β = 90
c = 168.594	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Saino, H., Ago, H., Miyano, M.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations