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- PDB-28my: Crystal structure of wild-type persulfide dioxygenase-rhodanese f... -

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Basic information

Entry
Database: PDB / ID: 28my
TitleCrystal structure of wild-type persulfide dioxygenase-rhodanese fusion CstB from Staphylococcus aureus: full-length structure - Cys201Ser/Cys408Ser double mutant
ComponentsCsoR-like sulfur transferase-regulated gene B
KeywordsMETAL BINDING PROTEIN / persulfide dioxygenase / rhodanese / hydrogen sulfide / reactive sulfur species / thiol persulfide / detoxyfication
Function / homology
Function and homology information


sulfur dioxygenase activity / hydrogen sulfide metabolic process / Hydrolases / glutathione metabolic process
Similarity search - Function
Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / : / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / MALONATE ION / SULFITE ION / CsoR-like sulfur transferase-regulated gene B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsCosta, S.S. / Campecino, J.O. / Giedroc, D.P. / Brito, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118157 United States
CitationJournal: Commun Chem / Year: 2026
Title: Self-S-sulfonation in a bacterial persulfide dioxygenase mediates thiol persulfide detoxification
Authors: 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. / ...Authors: 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.
History
DepositionFeb 9, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CsoR-like sulfur transferase-regulated gene B
B: CsoR-like sulfur transferase-regulated gene B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3607
Polymers103,9862
Non-polymers3745
Water54030
1
A: CsoR-like sulfur transferase-regulated gene B
B: CsoR-like sulfur transferase-regulated gene B
hetero molecules

A: CsoR-like sulfur transferase-regulated gene B
B: CsoR-like sulfur transferase-regulated gene B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,71914
Polymers207,9724
Non-polymers74810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10930 Å2
ΔGint-102 kcal/mol
Surface area67110 Å2
Unit cell
Length a, b, c (Å)147.648, 147.648, 124.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and resid 0 through 443)
d_2ens_1(chain "B" and resid 0 through 443)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 0 - 443 / Label seq-ID: 22 - 465

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.000358373720752, -0.994468013139, -0.105039242248), (-0.993898929229, -0.0112309940353, 0.109721389211), (-0.110294107031, 0.10443771166, -0.988396668518)Vector: 233. ...NCS oper: (Code: given
Matrix: (-0.000358373720752, -0.994468013139, -0.105039242248), (-0.993898929229, -0.0112309940353, 0.109721389211), (-0.110294107031, 0.10443771166, -0.988396668518)
Vector: 233.36536745, 221.257617595, 124.886551183)

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Components

#1: Protein CsoR-like sulfur transferase-regulated gene B / MBL fold metallo-hydrolase / Metal-dependent hydrolase with rhodanese-homology domain (RHOD) / ...MBL fold metallo-hydrolase / Metal-dependent hydrolase with rhodanese-homology domain (RHOD) / Metallo-beta-lactamase family protein / Persulfide dioxygenase-sulfurtransferase CstB / Zn-dependent hydrolase


Mass: 51992.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His-6 tag at N-terminus followed by a "DYDIPTTENLYFQGA" linker region. Numbering should start at G1, F2, F3, etc.
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: G5ELA4, Hydrolases
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 23 % (V/V) PEG 3350 0.1 M BisTris Propane pH 7.0 0.2 M Na.Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.48→104.4 Å / Num. obs: 25782 / % possible obs: 85.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.074 / Rrim(I) all: 0.268 / Net I/σ(I): 9.1
Reflection shellResolution: 2.48→3.01 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.328 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1289 / CC1/2: 0.46 / Rpim(I) all: 0.529 / Rrim(I) all: 1.438 / % possible all: 48.3

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Processing

Software
NameVersionClassification
autoPROC20250717data reduction
XDS20250714data reduction
pointless1.14.2data scaling
Aimless0.8.2data scaling
STARANISO3.0.12 (20250608)data scaling
PHASER2.8.3phasing
Coot0.9.8model building
BUSTER20250717refinement
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: SAD / Resolution: 2.48→104.4 Å / SU ML: 0.2247 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 1323 5.14 %
Rwork0.1968 24430 -
obs0.1985 25753 51.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.4 Å2
Refinement stepCycle: LAST / Resolution: 2.48→104.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7046 0 17 30 7093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247220
X-RAY DIFFRACTIONf_angle_d0.56589768
X-RAY DIFFRACTIONf_chiral_restr0.04481051
X-RAY DIFFRACTIONf_plane_restr0.00361289
X-RAY DIFFRACTIONf_dihedral_angle_d12.38522643
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.650005271542 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.560.507220.390617X-RAY DIFFRACTION0.41
2.58-2.600.54715X-RAY DIFFRACTION0.45
2.74-2.830.542930.368432X-RAY DIFFRACTION1.02
2.84-3.010.3179630.28851186X-RAY DIFFRACTION23.41
3.01-3.240.33272000.27943900X-RAY DIFFRACTION75.11
3.24-3.570.24642090.23914448X-RAY DIFFRACTION84.73
3.57-4.090.26982260.19764068X-RAY DIFFRACTION77.71
4.09-5.150.18083080.15245256X-RAY DIFFRACTION99.89
5.15-104.40.2163120.18185518X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04540583735-0.4531714680880.3374494321910.61353237395-0.2629577167820.4684515311920.03893942116430.2663372925450.0591690991355-0.180749375129-0.0508837335965-0.164737150198-0.01674581938650.171526956188-2.95029455493E-50.351560730199-0.03641117184680.04925949074880.414760172977-0.02520813148710.389386715462137.221757515110.5426955946.7339444906
20.521652118301-0.224134438947-0.1782529389120.8643855818120.4930759895650.598453854822-0.0539370351349-0.114489992317-0.1873460380480.2545621001610.0514666346144-0.001941366300930.221082214265-0.0303070410478-2.33649074136E-60.375177371409-0.0264533228489-0.0390042539820.3072883182670.01546071052120.388162993584118.73055954388.668679211174.1322914772
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 0 through 444)AA0 - 4441 - 445
22(chain 'B' and resid -10 through 443)BD-10 - 4431 - 454

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