5MX9 | pdb_00005mx9

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 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

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 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.
Department of Medical Microbiology and Infectious Disease, Cardiff Institute of Infection and Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, Wales.

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 
• Modeled 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 EC: 2.7.8.43
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 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

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
• Version 1.3: 2024-10-23
  Changes: Structure summary