3QDN | pdb_00003qdn

Putative thioredoxin protein from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb3QDN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-18 Released: 2011-02-09 
• Deposition Author(s): Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.302 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Putative thioredoxin protein from Salmonella typhimurium.

Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.77 kDa 
• Atom Count: 4,710 
• Modeled Residue Count: 565 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thioredoxin protein	A, B	287	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: STM0504, ybbN
UniProt
Find proteins for Q8ZR92 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZR92  Go to UniProtKB:  Q8ZR92

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.302 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33qdn

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.234	α = 90
b = 62.547	β = 98.66
c = 79.522	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary