2RFV | pdb_00002rfv

High resolution structure of L-methionine gamma-lyase from Citrobacter freundii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.177 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.146 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

High-resolution structure of methionine gamma-lyase from Citrobacter freundii.

Nikulin, A.Revtovich, S.Morozova, E.Nevskaya, N.Nikonov, S.Garber, M.Demidkina, T.

(2008) Acta Crystallogr D Biol Crystallogr 64: 211-218

  • DOI: https://doi.org/10.1107/S0907444907065390
  • Primary Citation Related Structures: 
    2RFV

  • PubMed Abstract: 

    Pyridoxal 5'-phosphate-dependent methionine gamma-lyase (MGL) is involved in the metabolism of sulfur-containing amino acids. The enzyme is a promising target in some anaerobic pathogens and is effective in cancer-cell treatment. The structure of the MGL holoenzyme from Citrobacter freundii has previously been determined at 1.9 A resolution. By modification of the crystallization procedure, the previously determined structure of C. freundii MGL has been improved to 1.35 A resolution with R and R(free) values of 0.152 and 0.177, respectively. This high-resolution structure makes it possible to analyze the interactions between the monomers in detail and to reveal the structurally invariant regions that are responsible for monomer-monomer recognition during the formation of the active enzyme. Details of the mode of cofactor binding and of the flexible regions that may be involved in substrate recognition and binding are also described.


  • Organizational Affiliation
    • Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.

Macromolecule Content 

  • Total Structure Weight: 43.29 kDa 
  • Atom Count: 3,552 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 398 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionine gamma-lyase398Citrobacter freundiiMutation(s): 0 
Gene Names: megL
EC: 4.4.1.11
UniProt
Find proteins for Q84AR1 (Citrobacter freundii)
Explore Q84AR1 
Go to UniProtKB:  Q84AR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84AR1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.177 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.146 (DCC) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.45α = 90
b = 122.8β = 90
c = 127.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection