3D4T

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

• PDB DOI: https://doi.org/10.2210/pdb3D4T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paracoccus denitrificans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-15 Released: 2008-07-15 
• Deposition Author(s): Carius, Y., Friedrich, C.G., Scheidig, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.216 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus indicates a dual Trx/Grx functionality for activation of chemotrophic sulfur oxidation in vivo

Carius, Y., Orawski, G., Bardischewsky, F., Quentmeier, A., Rother, D., Friedrich, C.G., Scheidig, A.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	116	Paracoccus denitrificans	Mutation(s): 0  Gene Names: soxS
UniProt
Find proteins for Q8KM22 (Paracoccus denitrificans) Explore Q8KM22  Go to UniProtKB:  Q8KM22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	B [auth A], C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.216 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81	α = 90
b = 81	β = 90
c = 33.1	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data collection
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Carius, Y., Friedrich, C.G., Scheidig, A.J.

Revision History  

• 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