9J90 | pdb_00009j90

Crystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in orthorhombic space group

PDB DOI: https://doi.org/10.2210/pdb9J90/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-21 Released: 2025-08-27
Deposition Author(s): Yadav, V.K., Shukla, M., Maji, S., Bhattacharyya, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.238 (Depositor), 0.227 (DCC)
R-Value Work:
0.179 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in orthorhombic space group

Yadav, V.K., Shukla, M., Maji, S., Bhattacharyya, S.

To be published.

Macromolecule Content

Total Structure Weight: 59.37 kDa
Atom Count: 4,118
Modeled Residue Count: 531
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nus factor SuhB	A [auth B], B [auth A]	271	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: suhB EC: 3.1.3.25
UniProt
Find proteins for Q9HXI4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXI4 Go to UniProtKB: Q9HXI4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HXI4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDE (Subject of Investigation/LOI) Query on GDE 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]	3,4,5-trihydroxybenzoic acid C₇ H₆ O₅ LNTHITQWFMADLM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DTV Query on DTV Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-QWWZWVQMSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.238 (Depositor), 0.227 (DCC)
R-Value Work: 0.179 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.681	α = 90
b = 90.108	β = 90
c = 90.453	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

Bhattacharyya, S.

Funding Organization	Location	Grant Number
Other government	India	S-12011/12/2021-SCHEME

Revision History (Full details and data files)

Version 1.0: 2025-08-27
Type: Initial release

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.