8STC | pdb_00008stc

S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with Zinc and soaked with bicarbonate.

• PDB DOI: https://doi.org/10.2210/pdb8STC/pdb

• Classification: LYASE
• Organism(s): Lactiplantibacillus plantarum WCFS1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-05-09 Released: 2024-07-03 
• Deposition Author(s): Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with Zinc and soaked with bicarbonate.

Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 159.14 kDa 
• Atom Count: 8,140 
• Modeled Residue Count: 1,203 
• Deposited Residue Count: 1,536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase	A, B, C, D, E, F	256	Lactiplantibacillus plantarum WCFS1	Mutation(s): 1  Gene Names: larB, lp_0105 EC: 2.5.1.143
UniProt
Find proteins for F9UST0 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UST0  Go to UniProtKB:  F9UST0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	H [auth A], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.38	α = 90
b = 120.38	β = 90
c = 213.159	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1807073
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM128959

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release