2QEZ | pdb_00002qez

Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2QEZ/pdb

• Classification: LYASE
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-26 Released: 2007-07-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.279 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 304.65 kDa 
• Atom Count: 20,573 
• Modeled Residue Count: 2,628 
• Deposited Residue Count: 2,730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine ammonia-lyase heavy chain	A, B, C, D, E, F	455	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: YP_013784.1, eutB, LMOf2365_1185 EC: 4.3.1.7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth C], J [auth D], K [auth D], L [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.279 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32QEZ

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.33	α = 90
b = 223.7	β = 90
c = 65.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-07-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary