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

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Basic information

Entry
Database: PDB / ID: 28mt
TitleCrystal structure of wild-type persulfide dioxygenase-rhodanese fusion CstB from Staphylococcus aureus: truncated structure - persulfidated Cys20
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
: / CsoR-like sulfur transferase-regulated gene B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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)99,1765
Polymers98,9992
Non-polymers1773
Water4,486249
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)198,35210
Polymers197,9984
Non-polymers3546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8660 Å2
ΔGint-136 kcal/mol
Surface area51350 Å2
Unit cell
Length a, b, c (Å)114.783, 114.783, 132.964
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

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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: 49499.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20 % (V/V) PEG 3350 0.02 M Na/K Phosphate pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→86.89 Å / Num. obs: 32247 / % possible obs: 49.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.063 / Rrim(I) all: 0.162 / Net I/σ(I): 8.8
Reflection shellResolution: 1.95→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1612 / CC1/2: 0.69 / Rpim(I) all: 0.392 / Rrim(I) all: 1.014 / % possible all: 6.9

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Processing

Software
NameVersionClassification
autoPROC20250717data reduction
XDSJan 19, 2025 (BUILT 20250714)data reduction
pointless1.14.2data scaling
Aimless0.8.2data scaling
STARANISO3.0.12 (20250608)data scaling
PHASER2.8.3phasing
Coot0.9.8model building
BUSTER2.10.4 (17-JUL-2025)refinement
PHENIX1.21.2-5419refinement
RefinementMethod to determine structure: SAD / Resolution: 1.95→86.89 Å / SU ML: 0.2116 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 1618 5.02 %
Rwork0.1781 30623 -
obs0.1805 32241 50 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.63 Å2
Refinement stepCycle: LAST / Resolution: 1.95→86.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5025 0 3 249 5277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585153
X-RAY DIFFRACTIONf_angle_d0.67926965
X-RAY DIFFRACTIONf_chiral_restr0.0473750
X-RAY DIFFRACTIONf_plane_restr0.0053903
X-RAY DIFFRACTIONf_dihedral_angle_d13.55631865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.391740.373666X-RAY DIFFRACTION1.32
2.01-2.070.2964140.2903217X-RAY DIFFRACTION4.35
2.07-2.140.2432200.2673394X-RAY DIFFRACTION7.76
2.14-2.230.3208210.2415573X-RAY DIFFRACTION11.12
2.23-2.330.2474500.2461913X-RAY DIFFRACTION17.89
2.33-2.450.322780.26911457X-RAY DIFFRACTION28.47
2.45-2.610.32021100.25542139X-RAY DIFFRACTION41.58
2.61-2.810.25252180.24354125X-RAY DIFFRACTION80.08
2.81-3.090.25632810.21595031X-RAY DIFFRACTION97.29
3.09-3.540.27522640.17315144X-RAY DIFFRACTION98.7
3.54-4.460.18522800.13665159X-RAY DIFFRACTION98.16
4.46-86.890.18142780.15765405X-RAY DIFFRACTION97.93
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)
12.016550743630.298425977935-0.5964807895272.29998949132-0.1336764978971.22941903034-0.1079911813230.01131797805140.0178579927829-0.01326315794060.0369975054803-0.02655719028450.087505695527-0.00080486856828-0.04559026856470.140740628045-0.0480160597893-0.05864459323880.009973692296830.03673682417050.0691399867699-14.2495239915-24.2070009793-14.2766214807
21.801378313030.377084704279-0.8175819375770.906806015017-0.034351213032.00989674145-0.04964057162910.2317053753770.109592783643-0.1993007070910.01784552393160.1360447198260.0230971385986-0.3515847073910.04115521697750.20135036836-0.120595130228-0.06473257317350.0706737194244-0.0007457870691560.105837384741-29.8566889085-28.0429907525-16.3662941001
30.730088338602-0.937789162817-0.2502824218132.16587161570.5390655695680.851221608439-0.1617280846110.1078866541940.2705624673890.1556302129520.0730563806455-0.0821778101076-0.161112899904-0.107601715098-0.08752964931670.263163057524-0.00364154516146-0.1201611890510.1294645223840.06065271771510.342393818199-15.94628042381.81158107052-18.2206927217
42.926204141950.9180922327880.245353772432.3902791591-0.2163057404042.832991957740.122068086246-0.164992387244-0.1214461251380.005119154212890.0026368379555-0.0470028792502-0.3877914768260.1304222237230.05765034978550.158235790863-0.129601787894-0.01563142430920.238047800954-0.03040507526530.11573559806213.136480497814.47739988116.7205790381
50.3245987081060.788183129822-0.7954621849362.08292803265-1.2631010644.378993431730.07754829485260.008452970959350.3741695839930.2327412862950.06014437553850.26040755006-1.23937594851-0.2865682076191.345175440180.701609103213-0.1099647703890.01784924587980.350310838928-0.07019431809960.35445919341711.646094714330.800536146411.3453254969
63.289487502630.3515365888071.169412122221.71577865485-0.3210929106451.987191535670.0806108998717-0.1956028116230.154337303625-0.0587257825694-0.0410627953940.0476659867109-0.304629696687-0.1128814338940.006741039534410.2044596260070.0564397887463-0.0250330135630.1635396095830.01492472605840.159620709905-15.797345197711.693490561510.9806189337
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 86 )AA1 - 861 - 86
22chain 'A' and (resid 87 through 255 )AA87 - 25587 - 228
33chain 'A' and (resid 256 through 345 )AA256 - 345229 - 318
44chain 'B' and (resid 1 through 168 )BD1 - 1681 - 156
55chain 'B' and (resid 169 through 255 )BD169 - 255157 - 227
66chain 'B' and (resid 256 through 345 )BD256 - 345228 - 317

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