4PXO

Crystal structure of Maleylacetoacetate isomerase from Methylobacteriu extorquens AM1 WITH BOUND MALONATE AND GSH (TARGET EFI-507068)

• PDB DOI: https://doi.org/10.2210/pdb4PXO/pdb

• Classification: TRANSFERASE
• Organism(s): Methylorubrum extorquens AM1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-24 Released: 2014-04-09 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.174 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Literature

Crystal structure of glutathione s-transferase zeta from Methylobacterium extorquens (TARGET EFI-507068)

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.9 kDa 
• Atom Count: 3,895 
• Modelled Residue Count: 430 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maleylacetoacetate isomerase (Glutathione S-transferase)	A, B	238	Methylorubrum extorquens AM1	Mutation(s): 0  Gene Names: maiA, MexAM1_META1p2830 EC: 2.5.1.18 (PDB Primary Data), 5.2.1.2 (PDB Primary Data)
UniProt
Find proteins for C5ATQ9 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATQ9  Go to UniProtKB:  C5ATQ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	D [auth A], I [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MLA	C [auth A], H [auth B]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.174 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.628	α = 90
b = 109.628	β = 90
c = 185.367	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Non-polymer description
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description