8AGA | pdb_00008aga

Structure of p-hydroxy benzoic acid ligand bound HosA transcriptional regulator from enteropathogenic Escherichia coli O127:H6 (strain E2348/69)

PDB DOI: https://doi.org/10.2210/pdb8AGA/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli O127:H6 str. E2348/69
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-19 Released: 2023-08-02
Deposition Author(s): Goswami, A., Kannika, B.R., Madan Kumar, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Horizontally acquired HosA transcription factor bound with 4-hydroxy-benzoic acid exhibits unique tug-of-water dynamics

Goswami, A., Ullah, S., Brito, J.A.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.04.24.590444

Macromolecule Content

Total Structure Weight: 16.83 kDa
Atom Count: 1,158
Modeled Residue Count: 131
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator HosA	A	143	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 0 Gene Names: hosA, E2348C_3010
UniProt
Find proteins for P69782 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore P69782 Go to UniProtKB: P69782
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69782
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHB (Subject of Investigation/LOI) Query on PHB 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]	P-HYDROXYBENZOIC ACID C₇ H₆ O₃ FJKROLUGYXJWQN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.38	α = 90
b = 67.38	β = 90
c = 95.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Madan Kumar, S.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection
Version 1.2: 2024-08-21
Changes: Database references, Structure summary
Version 1.3: 2026-03-04
Changes: Refinement description, Structure summary

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.