5E4Z

Crystal structure of methionine gamma-lyase from Citrobacter freundii with C115A substitution

• PDB DOI: https://doi.org/10.2210/pdb5E4Z/pdb

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


• Deposited: 2015-10-07 Released: 2016-10-12 
• Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.235 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Crystal structure of C115A mutant L-methionine gamma-lyase from Citrobacter freundii

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: 43.52 kDa 
• Atom Count: 3,131 
• Modelled Residue Count: 395 
• 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: AB180_17145, AB183_16780, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
1PE	B [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.235 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 122.631	β = 90
c = 127.296	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description