[English] 日本語
Yorodumi
- PDB-28mx: Crystal structure of wild-type persulfide dioxygenase-rhodanese f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 28mx
TitleCrystal structure of wild-type persulfide dioxygenase-rhodanese fusion CstB from Staphylococcus aureus: full-length structure - Cys408Ser 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)104,5569
Polymers104,0182
Non-polymers5387
Water2,756153
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)209,11218
Polymers208,0364
Non-polymers1,07614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area11630 Å2
ΔGint-91 kcal/mol
Surface area68000 Å2
Unit cell
Length a, b, c (Å)147.286, 147.286, 124.215
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

-
Components

-
Protein , 1 types, 2 molecules AB

#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: 52008.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His-6 tag at N-terminus followed by a "YDIPTTENLYFQGAM" 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

-
Non-polymers , 5 types, 160 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.02 %
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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.48→19.93 Å / Num. obs: 40074 / % possible obs: 95.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 41.73 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.078 / Rrim(I) all: 0.287 / Net I/σ(I): 9.2
Reflection shellResolution: 2.48→2.66 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.082 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2004 / CC1/2: 0.549 / Rpim(I) all: 0.583 / Rrim(I) all: 2.163 / % possible all: 63.3

-
Processing

Software
NameVersionClassification
autoPROC20250717data reduction
pointless1.13.6data 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→19.93 Å / SU ML: 0.2366 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 1987 4.96 %
Rwork0.1814 38087 -
obs0.183 40074 81.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.28 Å2
Refinement stepCycle: LAST / Resolution: 2.48→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7039 0 28 153 7220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00187222
X-RAY DIFFRACTIONf_angle_d0.43989767
X-RAY DIFFRACTIONf_chiral_restr0.0431049
X-RAY DIFFRACTIONf_plane_restr0.00341290
X-RAY DIFFRACTIONf_dihedral_angle_d11.81982644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.540.268690.2866152X-RAY DIFFRACTION4.64
2.54-2.610.341320.2906753X-RAY DIFFRACTION22.97
2.61-2.680.37191010.28371659X-RAY DIFFRACTION51.19
2.68-2.770.31291320.2622336X-RAY DIFFRACTION71.35
2.77-2.870.2781520.26462995X-RAY DIFFRACTION91.22
2.87-2.980.28651780.25923264X-RAY DIFFRACTION99.25
2.98-3.120.28341640.2343297X-RAY DIFFRACTION100
3.12-3.280.26021750.2123316X-RAY DIFFRACTION100
3.28-3.490.23561670.18373313X-RAY DIFFRACTION100
3.49-3.750.19411830.15653316X-RAY DIFFRACTION100
3.75-4.130.17241500.14353375X-RAY DIFFRACTION100
4.13-4.720.15991640.12953369X-RAY DIFFRACTION100
4.72-5.920.16031800.15043411X-RAY DIFFRACTION100
5.92-19.930.18812000.18513531X-RAY DIFFRACTION99.95
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)
11.40971670252-0.4935848769640.2262632179591.771694670410.2787835250131.586713550370.04614122147380.0680692228693-0.0071646335827-0.108946957234-0.0221461513528-0.260350229953-0.05034458658220.278211742323-0.0233424647010.167986999317-0.0294484685425-5.3826891685E-50.308412649488-0.02083306287040.372882336853144.780596168104.89560515858.6615391647
21.32721967094-0.488136233609-0.1327978286562.81297360459-0.4263069977760.5131638547310.06594981991020.3992704701660.037936894918-0.634833138723-0.0849379830924-0.1150772311330.03205225651140.2771022670140.01729072759020.393267313927-0.0208426996520.08043542638590.461791826514-0.02667491019110.439162944204146.973235667101.53706667143.6381272033
31.728789376550.06774273578730.6894882732081.340521983390.3515766126381.9430779510.01479953663980.4959778128640.0274509767648-0.3647195506270.0146291059785-0.225637039544-0.1262911601020.344663641171-0.03409814905010.320473109251-0.02360160983880.0950619078770.3641004303710.02521916865710.289275735591126.203862496118.24990320333.859883436
40.7211632133440.365226320701-0.214626382151.687623427940.171414227482.14851421443-0.02304009691790.0502909087604-0.0824959120374-0.1056524649350.0061456249702-0.0366276518369-0.05900389341040.04183715758960.003302097285820.256978066264-0.016999284364-0.03751250300570.203601139734-0.0324764389710.336106197311118.8088081189.028810969954.4366761929
51.48458583997-0.0710700784460.08903531270931.494277223020.2275177411921.441824804150.0801889560716-0.234897817186-0.2081032597910.170579808439-0.04283259614360.02202363971740.2012562752550.0326440296471-0.05816523958990.397022686752-0.00316511565679-0.04544562547320.212409242717-0.03793601033490.426428703552125.3975774877.555714390563.9896369198
62.78092357612-0.54507311265-0.3844600272811.31916506385-0.09807584532850.2945154952570.0189892950937-0.6563616610390.02701096889770.4152080369060.0553211492719-0.09259084496950.2299313660310.101692671283-0.0577283588840.4152015600310.0111610448379-0.0617000018980.366936973472-0.005370297704410.417543517221127.31029640678.387036787975.4098498311
71.832898876940.3673833121520.4644173954112.151927204230.7125690523592.425270352410.0144506498037-0.339015126042-0.2975550149340.528298854942-0.0123106614259-0.10403501870.3643611705280.0658871475411-0.008669282323160.371418012807-0.008851932869140.02223996824580.3103367129280.05792186851830.290483620866111.58495020497.778306759889.0661156104
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 212 )AA0 - 2121 - 213
22chain 'A' and (resid 213 through 255 )AA213 - 255214 - 256
33chain 'A' and (resid 256 through 444 )AA256 - 444257 - 445
44chain 'B' and (resid -9 through 79 )BD-9 - 791 - 89
55chain 'B' and (resid 80 through 212 )BD80 - 21290 - 222
66chain 'B' and (resid 213 through 255 )BD213 - 255223 - 265
77chain 'B' and (resid 256 through 443 )BD256 - 443266 - 453

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more