5D5S

Crystal structure of methionine gamma-lyase from Citrobacter freundii, S339A mutant

• PDB DOI: https://doi.org/10.2210/pdb5D5S/pdb

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


• Deposited: 2015-08-11 Released: 2016-08-17 
• Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.
• Funding Organization(s): RFBR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

The crystal structure of methionine gamma-lyase from Citrobacter freundii, S339A mutant

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: 43.35 kDa 
• Atom Count: 3,307 
• Modelled Residue Count: 380 
• 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: TN42_08855, TO64_18625 EC: 4.4.1.11
UniProt
Find proteins for A0A0A5P8W7 (Citrobacter freundii) Explore A0A0A5P8W7  Go to UniProtKB:  A0A0A5P8W7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.659	α = 90
b = 123.09	β = 90
c = 128.785	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.

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Funding Organization	Location	Grant Number
RFBR	Russian Federation	--

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description