2I4A | pdb_00002i4a

Crystal structure of thioredoxin from the acidophile Acetobacter aceti

• PDB DOI: https://doi.org/10.2210/pdb2I4A/pdb

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


• Deposited: 2006-08-21 Released: 2007-01-09 
• Deposition Author(s): Starks, C.M., Kappock, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.158 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Atomic-resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti.

Starks, C.M., Francois, J.A., Macarthur, K.M., Heard, B.Z., Kappock, T.J.

(2007) Protein Sci 16: 92-98

• PubMed: 17192591 
• DOI: https://doi.org/10.1110/ps.062519707
• Primary Citation Related Structures: 
  2I4A


• PubMed Abstract: 
  

  The crystal structure of thioredoxin (AaTrx) from the acetic acid bacterium Acetobacter aceti was determined at 1 A resolution. This is currently the highest resolution crystal structure available for any thioredoxin. Thioredoxins facilitate thiol-disulfide exchange, a process that is expected to be slow at the low pH values encountered in the A. aceti cytoplasm. Despite the apparent need to function at low pH, neither the active site nor the surface charge distribution of AaTrx is notably different from that of Escherichia coli thioredoxin. Apparently the ancestral thioredoxin was sufficiently stable for use in A. aceti or the need to interact with multiple targets constrained the variation of surface residues. The AaTrx structure presented here provides a clear view of all ionizable protein moieties and waters, a first step in understanding how thiol-disulfide exchange might occur in a low pH cytoplasm, and is a basis for biophysical studies of the mechanism of acid-mediated unfolding. The high resolution of this structure should be useful for computational studies of thioredoxin function, protein structure and dynamics, and side-chain ionization.

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Organizational Affiliation: 
• Department of Chemistry, Washington University in Saint Louis, Missouri 63130, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.65 kDa 
• Atom Count: 1,004 
• Modeled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thioredoxin	A	107	Acetobacter aceti	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.158 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/291

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.94	α = 90
b = 42.24	β = 90
c = 63.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
JBluIce-EPICS	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-09 
Deposition Author(s): Starks, C.M., Kappock, T.J.

Revision History  

• Version 1.0: 2007-01-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description