5NZ1

Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with sutezolid

• PDB DOI: https://doi.org/10.2210/pdb5NZ1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-12 Released: 2018-05-30 
• Deposition Author(s): Mendes, V., Blaszczyk, M., Nikiforov, P.O., Blundell, T.L.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.244 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

The antibiotics linezolid and sutezolid are ligands for Mycobacterium tuberculosis EthR

Nikiforov, P.O., Blaszczyk, M., Mendes, V., Boshoff, H.I., Barry, C.E., Blundell, T.L., Abell, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 203.13 kDa 
• Atom Count: 11,873 
• Modelled Residue Count: 1,522 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A, B, C, D, E, F, G, H	228	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ethR, etaR, Rv3855
UniProt
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMC1  Go to UniProtKB:  P9WMC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9EN	I [auth A], J [auth C], K [auth D]	~{N}-[[(5~{S})-3-(3-fluoranyl-4-thiomorpholin-4-yl-phenyl)-2-oxidanylidene-1,3-oxazolidin-5-yl]methyl]ethanamide C16 H20 F N3 O3 S FNDDDNOJWPQCBZ-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.244 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.858	α = 90
b = 144.841	β = 90
c = 150.741	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Mendes, V., Blaszczyk, M., Nikiforov, P.O., Blundell, T.L.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description