3D4T | pdb_00003d4t

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (oxidized form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

The structure of the periplasmic thiol-disulfide oxidoreductase SoxS from Paracoccus pantotrophus indicates a triple Trx/Grx/DsbC functionality in chemotrophic sulfur oxidation.

Carius, Y.Rother, D.Friedrich, C.G.Scheidig, A.J.

(2009) Acta Crystallogr D Biol Crystallogr 65: 229-240

  • DOI: https://doi.org/10.1107/S0907444908043023
  • Primary Citation Related Structures: 
    3D4T, 3DML

  • PubMed Abstract: 

    The periplasmic thiol-disulfide oxidoreductase SoxS is beneficial for the sulfur-oxidizing (Sox) phenotype of the facultative chemotrophic bacterium Paracoccus pantotrophus and is not part of the Sox enzyme system. SoxS combines features of thioredoxins, glutaredoxins and the thiol-disulfide oxidoreductases of the Dsb family in structure, target specificity and reaction. The structure of SoxS was solved in oxidized and reduced forms at 2.1 and 1.9 A resolution, respectively. SoxS revealed high structural homology to typical cytoplasmic bacterial thioredoxins. In contrast, SoxS contained the active-site motif Pro-Gly-Cys-Leu-Tyr-Cys that is not present in other thioredoxins. Interestingly, the sequence of this motif is closely related to the Pro-Gly-Cys-Pro-Tyr-Cys sequence of some glutaredoxins and to the Pro-Xaa-Cys-Xaa-Tyr-Cys sequences of some members of the DsbC and DsbG subfamilies of thiol-disulfide oxidoreductases. Furthermore, the proposed substrate of SoxS, the interprotein disulfide of SoxY, Cys110(Y)-Cys110(Y), is structurally similar to oxidized glutathione. However, SoxS is proposed to specifically reduce the interprotein disulfide between two SoxY subunits, releasing a heterodimeric SoxYZ as an active part of the sulfur-oxidation cycle.


  • Organizational Affiliation
    • Abteilung für Strukturbiologie, Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.

Macromolecule Content 

  • Total Structure Weight: 13.24 kDa 
  • Atom Count: 904 
  • Modeled Residue Count: 97 
  • Deposited Residue Count: 116 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein116Paracoccus denitrificansMutation(s): 0 
Gene Names: soxS
UniProt
Find proteins for Q8KM22 (Paracoccus denitrificans)
Explore Q8KM22 
Go to UniProtKB:  Q8KM22
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KM22
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81α = 90
b = 81β = 90
c = 33.1γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2025-08-06
    Changes: Database references, Structure summary