4PFZ | pdb_00004pfz

X-ray Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb4PFZ/pdb

• Classification: ISOMERASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-01 Released: 2014-11-19 
• Deposition Author(s): Horanyi, P.S., Abendroth, J., Lorimer, D., Edwards, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase from Mycobacterium smegmatis

Horanyi, P.S., Abendroth, J., Lorimer, D., Edwards, T.

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: 55.41 kDa 
• Atom Count: 4,079 
• Modeled Residue Count: 501 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-carboxymethyl-2-hydroxymuconate delta-isomerase	A, B	259	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_2382, MSMEI_2322
UniProt
Find proteins for A0QUY6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QUY6  Go to UniProtKB:  A0QUY6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34PFZ

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137	α = 90
b = 53.74	β = 107.76
c = 69.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Horanyi, P.S., Abendroth, J., Lorimer, D., Edwards, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy