28MY | pdb_000028my

Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion CstB from Staphylococcus aureus: full-length structure - Cys201Ser/Cys408Ser double mutant

• PDB DOI: https://doi.org/10.2210/pdb28MY/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 104.36 kDa 
• Atom Count: 7,093 
• Modeled Residue Count: 899 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

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, 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI (Subject of Investigation/LOI)	G [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
SO3 (Subject of Investigation/LOI)	D [auth A], F [auth B]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.648	α = 90
b = 147.648	β = 90
c = 124.901	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Costa, S.S., Campecino, J.O., Giedroc, D.P., Brito, J.A.

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

Revision History  

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