5IDH | pdb_00005idh

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8-bromooctanoic acid

• PDB DOI: https://doi.org/10.2210/pdb5IDH/pdb

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


• Deposited: 2016-02-24 Released: 2017-03-15 
• Deposition Author(s): Hughes, S.J., Song, J.H., Antoshchenko, T., Park, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8-bromooctanoic acid

Hughes, S.J., Song, J.H., Antoshchenko, T., 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)

Macromolecule Content 

• Total Structure Weight: 40.77 kDa 
• Atom Count: 3,004 
• Modeled Residue Count: 316 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoate--protein ligase	A	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
SH6	B [auth A]	8-bromooctanoic acid C8 H15 Br O2 BKJFDZSBZWHRNH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.968	α = 90
b = 67.757	β = 115.73
c = 54.193	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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