5NZ0 | pdb_00005nz0

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

PDB DOI: https://doi.org/10.2210/pdb5NZ0/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): Blaszczyk, M., Mendes, V., Nikiforov, P.O., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.220 (Depositor), 0.221 (DCC)
R-Value Work:
0.184 (Depositor), 0.187 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5NZ0

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 25.66 kDa
Atom Count: 1,632
Modeled Residue Count: 190
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WMC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZLD Query on ZLD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide C₁₆ H₂₀ F N₃ O₄ TYZROVQLWOKYKF-ZDUSSCGKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.220 (Depositor), 0.221 (DCC)
R-Value Work: 0.184 (Depositor), 0.187 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.382	α = 90
b = 121.382	β = 90
c = 33.78	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Nikiforov, P.O.

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.