5MX9

High resolution crystal structure of the MCR-2 catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb5MX9/pdb

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


• Deposited: 2017-01-22 Released: 2017-08-09 
• Deposition Author(s): Hinchliffe, P., Coates, K., Walsh, T.R., Spencer, J.
• Funding Organization(s): Medical Research Council (United Kingdom)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.145 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 

Starting Model: experimental

Literature

1.12 angstrom resolution crystal structure of the catalytic domain of the plasmid-mediated colistin resistance determinant MCR-2.

Coates, K., Walsh, T.R., Spencer, J., Hinchliffe, P.

(2017) Acta Crystallogr F Struct Biol Commun 73: 443-449

• PubMed: 28777086 
• DOI: https://doi.org/10.1107/S2053230X17009669
• Primary Citation of Related Structures:  
  5MX9


• PubMed Abstract: 
  

  MCR-2 confers resistance to colistin, a `last-line' antibiotic against extensively resistant Gram-negative pathogens. It is a plasmid-encoded phosphoethanolamine transferase that is closely related to MCR-1. To understand the diversity in the MCR family, the 1.12 Å resolution crystal structure of the catalytic domain of MCR-2 was determined. Variable amino acids are located distant from both the di-zinc active site and the membrane-proximal face. The exceptionally high resolution will provide an accurate starting model for further mechanistic studies.

---

Organizational Affiliation: 

School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, England.

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: 36.49 kDa 
• Atom Count: 3,004 
• Modelled Residue Count: 324 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylethanolamine transferase Mcr-2	A	324	Escherichia coli	Mutation(s): 0  Gene Names: mcr-2
UniProt
Find proteins for A0A1C3NEV1 (Escherichia coli) Explore A0A1C3NEV1  Go to UniProtKB:  A0A1C3NEV1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.145 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.818	α = 90
b = 53.31	β = 90
c = 117.509	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Hinchliffe, P., Coates, K., Walsh, T.R., Spencer, J.

---

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/P007295/1

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description