5ICL

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with lipoyl-AMP

• PDB DOI: https://doi.org/10.2210/pdb5ICL/pdb

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


• Deposited: 2016-02-23 Released: 2017-03-15 
• Deposition Author(s): Hughes, S.J., Antoshchenko, T., Song, J.H., Park, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with lipoyl-AMP

Hughes, S.J., Antoshchenko, T., Song, J.H., Park, H.W.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.17 kDa 
• Atom Count: 5,744 
• Modelled Residue Count: 641 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoate--protein ligase	A, B	352	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: lplA-2, EF_2741 EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for Q830N7 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830N7  Go to UniProtKB:  Q830N7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LAQ	C [auth A], D [auth B]	5'-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE C18 H26 N5 O8 P S2 QWEGOCJRZOKSOE-ADUAKINBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.942	α = 90
b = 69.35	β = 92.15
c = 97.685	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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