5IJ6 | pdb_00005ij6

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-1) in complex with lipoic acid

• PDB DOI: https://doi.org/10.2210/pdb5IJ6/pdb

• Classification: LIGASE,TRANSFERASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-01 Released: 2017-03-15 
• Deposition Author(s): Hughes, S.J., Lyle, A.G., Song, J.H., Antoshchenko, T., Park, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-1) in complex with lipoic acid

Hughes, S.J., Lyle, A.G., Antoshchenko, T., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 41.12 kDa 
• Atom Count: 2,815 
• Modeled Residue Count: 322 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoate--protein ligase	A	355	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: lplA-1, EF_0650 EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for Q838C1 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838C1  Go to UniProtKB:  Q838C1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LPA	B [auth A]	LIPOIC ACID C8 H14 O2 S2 AGBQKNBQESQNJD-SSDOTTSWSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.011	α = 90
b = 70.912	β = 90
c = 106.466	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Hughes, S.J., Lyle, A.G., Song, J.H., Antoshchenko, T., Park, H.

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description