5IBY

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

PDB DOI: https://doi.org/10.2210/pdb5IBY/pdb

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

Deposited: 2016-02-22 Released: 2017-03-15
Deposition Author(s): Hughes, S.J., Song, J.H., Antoshchenko, T., Park, H.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.210
R-Value Work: 0.164
R-Value Observed: 0.166

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 40.76 kDa
Atom Count: 2,971
Modelled Residue Count: 321
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q830N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LPA Query on LPA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	LIPOIC ACID C₈ H₁₄ O₂ S₂ AGBQKNBQESQNJD-SSDOTTSWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.210
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.977	α = 90
b = 68.561	β = 116.13
c = 54.154	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Antoshchenko, T.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.