4OZE

A.aolicus LpxC in complex with native product

• PDB DOI: https://doi.org/10.2210/pdb4OZE/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-02-15 Released: 2014-08-13 
• Deposition Author(s): Olivier, N.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.185 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

Mechanistic insight from the crystal structure of A.aolicus LpxC in the presence of product

Miller, M.D., Gao, N., Ross, P., Olivier, N.B.

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: 66.5 kDa 
• Atom Count: 5,058 
• Modelled Residue Count: 533 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B	282	Aquifex aeolicus	Mutation(s): 0  Gene Names: lpxC, envA, aq_1772 EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5)) Explore O67648  Go to UniProtKB:  O67648

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
24G	H [auth A], M [auth B]	uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine C29 H51 N3 O18 P2 ZFPNNOXCEDQJQS-SSVOXRMNSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.185 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.332	α = 90
b = 101.332	β = 90
c = 123.553	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Olivier, N.B.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy