5NZ1 | pdb_00005nz1

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.244 (Depositor), 0.255 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 203.13 kDa
Atom Count: 11,873
Modeled Residue Count: 1,522
Deposited Residue Count: 1,824
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, B, C, D, E 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
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9EN Query on 9EN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	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		Interactions Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.244 (Depositor), 0.255 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.194 (Depositor)

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

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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

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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.