28MX | pdb_000028mx

Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion CstB from Staphylococcus aureus: full-length structure - Cys408Ser mutant

PDB DOI: https://doi.org/10.2210/pdb28MX/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-09 Released: 2026-10-14
Deposition Author(s): Costa, S.S., Campecino, J.O., Giedroc, D.P., Brito, J.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.212 (Depositor), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.191 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 28MX

Ligand Structure Quality Assessment

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

Literature

Self-S-sulfonation in a bacterial persulfide dioxygenase mediates thiol persulfide detoxification

Campecino, J.O., Costa, S.S., Pires, I.D.S., Walsh, B.J.C., Trinidad, J.C., Kannoujia, J., Poore, A.T., Van Stappen, C., Gonzalez-Gutierrez, G., Archer, M., Machuqueiro, M., Brito, J.A., Giedroc, D.P.

(2026) Commun Chem

DOI: https://doi.org/10.1038/s42004-026-02216-y

Macromolecule Content

Total Structure Weight: 104.56 kDa
Atom Count: 7,221
Modeled Residue Count: 898
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CsoR-like sulfur transferase-regulated gene B	A, B	466	Staphylococcus aureus	Mutation(s): 0 Gene Names: cstB, pksB, ACR79_07025, CNH36_00185, DQU50_10665, EIH03_09430, EP54_06780, EQ90_14360, G6Y24_10060, GO793_08295... cstB, pksB, ACR79_07025, CNH36_00185, DQU50_10665, EIH03_09430, EP54_06780, EQ90_14360, G6Y24_10060, GO793_08295, GO814_02890, GO941_08520, GO942_14170, GQX52_14545, GZ130_12005, M1K003_0679, SAMEA4552975_01688, SAMEA70153168_00919 EC: 3
UniProt
Find proteins for G5ELA4 (Staphylococcus aureus) Explore G5ELA4 Go to UniProtKB: G5ELA4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G5ELA4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI (Subject of Investigation/LOI) Query on MLI Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
SO3 (Subject of Investigation/LOI) Query on SO3 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.212 (Depositor), 0.220 (DCC)
R-Value Work: 0.181 (Depositor), 0.191 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.286	α = 90
b = 147.286	β = 90
c = 124.215	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
pointless	data scaling
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building
BUSTER	refinement
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Campecino, J.O.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118157

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release