1E5E | pdb_00001e5e

METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS IN COMPLEX WITH PROPARGYLGLYCINE

• PDB DOI: https://doi.org/10.2210/pdb1E5E/pdb

• Classification: LYASE
• Organism(s): Trichomonas vaginalis G3
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2000-07-25 Released: 2001-07-19 
• Deposition Author(s): Goodall, G., Mottram, J.C., Coombs, G.H., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.193 (Depositor) 
• R-Value Work: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

The Structure and Proposed Catalytic Mechanism of Methionine Gamma-Lyase

Goodall, G., Mottram, J.C., Coombs, G.H., Lapthorn, A.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 89.69 kDa 
• Atom Count: 6,933 
• Modeled Residue Count: 787 
• Deposited Residue Count: 808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONINE GAMMA-LYASE	A, B	404	Trichomonas vaginalis G3	Mutation(s): 0  Gene Names: MGL1 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.1 (UniProt)
UniProt
Find proteins for A2FEV4 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2FEV4  Go to UniProtKB:  A2FEV4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPJ	C [auth A], G [auth B]	N-(HYDROXY{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)NORVALINE C13 H19 N2 O8 P XZPXXYMXESJHME-PMICCBOBSA-N
SO4	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.193 (Depositor) 
• R-Value Work:  0.140 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.258	α = 90
b = 88.258	β = 90
c = 217.849	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-19 
Deposition Author(s): Goodall, G., Mottram, J.C., Coombs, G.H., Lapthorn, A.J.

Revision History  

• Version 1.0: 2001-07-19
  Type: Initial release
  
• Version 1.1: 2011-11-09
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2014-02-05
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary