7YSI

Crystal structure of thioredoxin 2

• PDB DOI: https://doi.org/10.2210/pdb7YSI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-08-12 Released: 2023-03-15 
• Deposition Author(s): Chang, Y.J., Park, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.188 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Literature

Comparison of the structure and activity of thioredoxin 2 and thioredoxin 1 from Acinetobacter baumannii.

Chang, Y.J., Sung, J.H., Lee, C.S., Lee, J.H., Park, H.H.

(2023) IUCrJ 10: 147-155

• PubMed: 36752373 
• DOI: https://doi.org/10.1107/S2052252523000404
• Primary Citation of Related Structures:  
  7YSI


• PubMed Abstract: 
  

  Thioredoxin (Trx) is essential in a redox-control system, with many bacteria containing two Trxs: Trx1 and Trx2. Due to a Trx system's critical function, Trxs are targets for novel antibiotics. Here, a 1.20 Å high-resolution structure of Trx2 from Acinetobacter baumannii (abTrx2), an antibiotic resistant pathogenic superbug, is elucidated. By comparing Trx1 and Trx2, it is revealed that the two Trxs possess similar activity, although Trx2 contains an additional N-terminal zinc-finger domain and exhibits more flexible properties in solution. Finally, it is shown that the Trx2 zinc-finger domain might be rotatable and that proper zinc coordination at the zinc-finger domain is critical to abTrx2 activity. This study enhances understanding of the Trx system and will facilitate the design of novel antibiotics.

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Organizational Affiliation: 

College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 16.87 kDa 
• Atom Count: 1,341 
• Modelled Residue Count: 143 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol disulfide reductase thioredoxin	A	149	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  trxC, AYR68_15440, B7L45_02985, BAA1790NC_0521, BS065_02615, CBL15_02595, CTZ19_02595, D8O08_003970, DLI71_14475, DLI72_02635, E2532_03525, E2533_03310, E2534_07555, E2535_02615, E2536_10370, E2538_07040, E2539_06760, E2540_11860, E2541_06480, EA720_013275, FDN00_17805, FE003_02610, IAG11_14015
UniProt
Find proteins for A0A219CD23 (Acinetobacter baumannii) Explore A0A219CD23  Go to UniProtKB:  A0A219CD23

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.188 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.59	α = 90
b = 55.01	β = 90
c = 78.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Chang, Y.J., Park, H.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description