3AEJ | pdb_00003aej

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 tetramer containing Michaelis complex and methionine-pyridoxal-5'-phosphate

• PDB DOI: https://doi.org/10.2210/pdb3AEJ/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: 2.59 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

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: 12,308 
• Modeled Residue Count: 1,544 
• Deposited Residue Count: 1,556 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B, D	389	Entamoeba histolytica	Mutation(s): 0  Gene Names: metg EC: 4.4.1.11 (PDB Primary Data), 2.5.1.160 (UniProt)
UniProt
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28  Go to UniProtKB:  Q86D28

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	C	389	Entamoeba histolytica	Mutation(s): 0  Gene Names: metg EC: 4.4.1.11 (PDB Primary Data), 2.5.1.160 (UniProt)
UniProt
Find proteins for Q86D28 (Entamoeba histolytica) Explore Q86D28  Go to UniProtKB:  Q86D28

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AA5	E [auth A], H [auth B], M [auth D]	N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE C13 H19 N2 O7 P S HPCOPQVFKQIVQF-DMSFABOWSA-N
MET	J [auth C]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
SO4	F [auth A], I [auth B], K [auth C], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	C	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.738	α = 90
b = 85.359	β = 101.92
c = 113.664	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
• Version 1.4: 2023-11-15
  Changes: Data collection