4HF8

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

Structural Biology Knowledgebase: 4HF8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.337
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 4HF8

Classification: LYASE

Total Structure Weight: 43722.96

Macromolecule Entities
Molecule Chains Length Organism Details
Methionine gamma-lyase A 398 Citrobacter freundii EC#: 4.4.1.11 IUBMB
Mutation: L133F, G137A
Gene Name(s): megL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLG
Query on PLG

A N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4-YL-METHANE]
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE (Synonym)
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLY
Query on GLY

A GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.337
  • R-Value Work: 0.224
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.29 α = 90.00
b = 123.05 β = 90.00
c = 126.75 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-05
  • Released Date: 2013-11-06
  • Deposition author(s): Revtovich, S.V., Morozova, E.A., Anufrieva, N.V., Nikulin, A.D., Demidkina, T.V.

Revision History

  • 2014-11-12
    Type: Citation | Details: Citation update