7NGK | pdb_00007ngk

Mycobacterium tuberculosis transcriptional regulator EthR with bound inhibitory compound

PDB DOI: https://doi.org/10.2210/pdb7NGK/pdb

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

Deposited: 2021-02-09 Released: 2022-02-23
Deposition Author(s): Tomlinson, C.W.E., Tatum, N.J., Pohl, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.222 (Depositor), 0.221 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Systematic exploration of the hydrophobic capacity of the EthR binding site for lead compound optimization

Tatum, N.J., Tomlinson, C.W.E., Frita, R., Bennett, R., Baulard, A.R., Pohl, E., Kitching, M.O.

To be published.

Macromolecule Content

Total Structure Weight: 24.1 kDa
Atom Count: 1,635
Modeled Residue Count: 193
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A	216	Mycobacterium tuberculosis	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
UAE (Subject of Investigation/LOI) Query on UAE 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]	~{N}-cyclohexyl-4-methyl-piperidine-1-carboxamide C₁₃ H₂₄ N₂ O BOSHLBWKQSSSGD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.222 (Depositor), 0.221 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.164	α = 90
b = 121.164	β = 90
c = 33.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
pointless	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Tomlinson, C.W.E.

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.