1Y4I

Crystal structure of Citrobacter Freundii L-methionine-lyase

• PDB DOI: https://doi.org/10.2210/pdb1Y4I/pdb

• Classification: LYASE
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-12-01 Released: 2005-06-14 
• Deposition Author(s): Revtovich, S.V., Mamaeva, D.V., Morozova, E.A., Nikulin, A.D., Nikonov, S.V., Garber, M.B., Demidkina, T.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Structure of Citrobacter freundii L-methionine gamma-lyase.

Mamaeva, D.V., Morozova, E.A., Nikulin, A.D., Revtovich, S.V., Nikonov, S.V., Garber, M.B., Demidkina, T.V.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 546-549

• PubMed: 16511092 
• DOI: https://doi.org/10.1107/S1744309105015447
• Primary Citation of Related Structures:  
  1Y4I


• PubMed Abstract: 
  

  L-Methionine gamma-lyase (MGL) is a pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyzes gamma-elimination of L-methionine. The crystal structure of MGL from Citrobacter freundii has been determined at 1.9 A resolution. The spatial fold of the protein is similar to those of MGLs from Pseudomonas putida and Trichomonas vaginalis. The comparison of these structures revealed that there are differences in PLP-binding residues and positioning of the surrounding flexible loops.

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Organizational Affiliation: 

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 43.32 kDa 
• Atom Count: 3,133 
• Modelled Residue Count: 397 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methionine gamma-lyase	A	398	Citrobacter freundii	Mutation(s): 1  Gene Names: megL EC: 4.4.1.11
UniProt
Find proteins for Q84AR1 (Citrobacter freundii) Explore Q84AR1  Go to UniProtKB:  Q84AR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.35	α = 90
b = 121.83	β = 90
c = 127.16	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Revtovich, S.V., Mamaeva, D.V., Morozova, E.A., Nikulin, A.D., Nikonov, S.V., Garber, M.B., Demidkina, T.V.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection