3PMO | pdb_00003pmo

The structure of LpxD from Pseudomonas aeruginosa at 1.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3PMO/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-17 Released: 2011-07-27 
• Deposition Author(s): Badger, J., Chie-Leon, B., Logan, C., Sridhar, V., Sankaran, B., Zwart, P.H., Nienaber, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

The structure of LpxD from Pseudomonas aeruginosa at 1.3 A resolution.

Badger, J., Chie-Leon, B., Logan, C., Sridhar, V., Sankaran, B., Zwart, P.H., Nienaber, V.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 749-752

• PubMed: 21795786 
• DOI: https://doi.org/10.1107/S1744309111018811
• Primary Citation Related Structures: 
  3PMO


• PubMed Abstract: 
  

  LpxD is a bacterial protein that is part of the biosynthesis pathway of lipid A and is responsible for transferring 3-hydroxymyristic acid from the R-3-hydroxymyristoyl-acyl carrier protein to the 2-OH group of UDP-3-O-(3-hydroxymyristoyl) glucosamine. The crystal structure of LpxD from Pseudomonas aeruginosa has been determined at high resolution (1.3 Å). The crystal belonged to space group H3, with unit-cell parameters a=b=106.19, c=93.38 Å, and contained one molecule in the asymmetric unit. The structure was solved by molecular replacement using the known structure of LpxD from Escherichia coli (PDB entry 3eh0) as a search model and was refined to Rwork=16.4% (Rfree=18.5%) using 91,655 reflections. The final protein model includes 355 amino-acid residues (including 16 amino acids from a 20 amino-acid N-terminal His tag), one chloride ion and two ethylene glycol molecules.

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Organizational Affiliation: 
• Zenobia Therapeutics, 505 Coast Boulevard South, Suite 111, La Jolla, CA 92122, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 38.43 kDa 
• Atom Count: 3,116 
• Modeled Residue Count: 357 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase	A	372	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: lpxD, PA3646 EC: 2.3.1 (PDB Primary Data), 2.3.1.191 (UniProt)
UniProt
Find proteins for Q9HXY6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXY6  Go to UniProtKB:  Q9HXY6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.19	α = 90
b = 106.19	β = 90
c = 93.38	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Badger, J., Chie-Leon, B., Logan, C., Sridhar, V., Sankaran, B., Zwart, P.H., Nienaber, V.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations