1UKJ | pdb_00001ukj

Detailed structure of L-Methionine-Lyase from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb1UKJ/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-08-24 Released: 2004-10-19 
• Deposition Author(s): Misaki, S., Takimoto, A., Takakura, T., Yoshioka, T., Yamashita, M., Tamura, T., Tanaka, H., Inagaki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.295 (Depositor) 
• R-Value Work: 
  0.177 (Depositor) 

Literature

Detailed structure of L-Methionine -Lyase from Pseudomonas putida

Misaki, S., Takimoto, A., Takakura, T., Yoshioka, T., Yamashita, M., Tamura, T., Tanaka, H., Inagaki, K.

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: 172.09 kDa 
• Atom Count: 13,148 
• Modelled Residue Count: 1,592 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B, C, D	398	Pseudomonas putida	Mutation(s): 1  EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for P13254 (Pseudomonas putida) Explore P13254  Go to UniProtKB:  P13254

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth B], H [auth C], I [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.295 (Depositor) 
• R-Value Work:  0.177 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.093	α = 90
b = 133.093	β = 90
c = 215.028	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-19 
Deposition Author(s): Misaki, S., Takimoto, A., Takakura, T., Yoshioka, T., Yamashita, M., Tamura, T., Tanaka, H., Inagaki, K.

Revision History  

• Version 1.0: 2004-10-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations