4P7Y | pdb_00004p7y

L-methionine gamma-lyase from Citrobacter freundii with Y58F substitution

• PDB DOI: https://doi.org/10.2210/pdb4P7Y/pdb

• Classification: LYASE
• Organism(s): Citrobacter freundii GTC 09479
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2014-03-28 Released: 2014-11-12 
• Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.
• Funding Organization(s): Russian Foundation for Basci Research

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with Y58F substitution

Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.

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: 43.23 kDa 
• Atom Count: 3,268 
• Modeled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONINE GAMMA-LYASE	A	396	Citrobacter freundii GTC 09479	Mutation(s): 1  Gene Names: H262_14272

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.546	α = 90
b = 124.531	β = 90
c = 129.874	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.

---

Funding Organization	Location	Grant Number
Russian Foundation for Basci Research	Russian Federation	--

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 2.0: 2018-03-21
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2023-11-15
  Changes: Data collection