3AEL

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing methionine imine-pyridoxamine-5'-phosphate and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate

• PDB DOI: https://doi.org/10.2210/pdb3AEL/pdb

• Classification: LYASE
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-10 Released: 2011-02-09 
• Deposition Author(s): Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.188 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Crystal structure of Entamoeba histolytica methionine gamma-lyase 1

Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.

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: 171.48 kDa 
• Atom Count: 12,836 
• Modelled Residue Count: 1,544 
• Deposited Residue Count: 1,556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B, C, D	389	Entamoeba histolytica	Mutation(s): 0  Gene Names: metg EC: 4.4.1.11
UniProt
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28  Go to UniProtKB:  Q86D28

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2LM	I [auth B], K [auth C], N [auth D]	(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid C13 H19 N2 O7 P S RNHGWTJOZCEIDD-RVDMUPIBSA-N
4LM	E [auth A]	(2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid C12 H15 N2 O7 P BBYSOXSBJOWRNU-VMTXVVAMSA-N
SO4	G [auth A], J [auth B], L [auth C], O [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MEE	F [auth A]	METHANETHIOL C H4 S LSDPWZHWYPCBBB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.188 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.965	α = 90
b = 85.22	β = 101.98
c = 114.253	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Karaki, T., Sato, D., Shimizu, A., Nozaki, T., Harada, S.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description