Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal structure of thioredoxin from Escherichia coli at 1.68 A resolution.

Katti, S.K.LeMaster, D.M.Eklund, H.

(1990) J Mol Biol 212: 167-184

  • DOI: 10.1016/0022-2836(90)90313-B
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of thioredoxin from Escherichia coli has been refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.165 at 1.68 A resolution. In the final model, the root-mean-square deviation fr ...

    The crystal structure of thioredoxin from Escherichia coli has been refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.165 at 1.68 A resolution. In the final model, the root-mean-square deviation from ideality for bond distances is 0.015 A and for angle distances 0.035 A. The structure contains 1644 protein atoms from two independent molecules, two Cu2+, 140 water molecules and seven methylpentanediol molecules. Ten residues have been modeled in two alternative conformations. E. coli thioredoxin is a compact molecule with 90% of its residues in helices, beta-strands or reverse turns. The molecule consists of two conformational domains, beta alpha beta alpha beta and beta beta alpha, connected by a single-turn alpha-helix and a 3(10) helix. The beta-sheet forms the core of the molecule packed on either side by clusters of hydrophobic residues. Helices form the external surface. The active site disulfide bridge between Cys32 and Cys35 is located at the amino terminus of the second alpha-helix. The positive electrostatic field due to the helical dipole is probably important for stabilizing the anionic intermediate during the disulfide reductase function of the protein. The more reactive cysteine, Cys32, has its sulfur atom exposed to solvent and also involved in a hydrogen bond with a backbone amide group. Residues 29 to 37, which include the active site cysteine residues, form a protrusion on the surface of the protein and make relatively fewer interactions with the rest of the structure. The disulfide bridge exhibits a right-handed conformation with a torsion angle of 81 degrees and 72 degrees about the S-S bond in the two molecules. Twenty-five pairs of water molecules obey the noncrystallographic symmetry. Most of them are involved in establishing intramolecular hydrogen-bonding interactions between protein atoms and thus serve as integral parts of the folded protein structure. Methylpentanediol molecules often pack against the loops and stabilize their structure. Cu2+ used for crystallization exhibit a distorted octahedral square bipyramid co-ordination and provide essential packing interactions in the crystal. The two independent protein molecules are very similar in conformation but distinctly different in atomic detail (root-mean-square = 0.94 A). The differences, which may be related to the crystal contacts, are localized mostly to regions far from the active site.

    Related Citations: 
    • Three-Dimensional Structure of Escherichia Coli Thioredoxin-S2 to 2.8 Angstroms Resolution
      Holmgren, A., Soderberg, B.-O., Eklund, H., Branden, C.-I.
      (1975) Proc Natl Acad Sci U S A 72: 2305
    • Structure of Oxidized Thioredoxin to 4.5 Angstroms Resolution
      Soderberg, B.-O., Holmgren, A., Branden, C.-I.
      (1974) J Mol Biol 90: 143
    • Crystallization and Preliminary Crystallographic Data for Thioredoxin from Escherichia Coli B
      Holmgren, A., Soderberg, B.-O.
      (1970) J Mol Biol 54: 387

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THIOREDOXINAB108Escherichia coliMutation(s): 0 
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download CCD File 
A, B
C6 H14 O2
 Ligand Interaction
Query on CU

Download CCD File 
A, B
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.5α = 90
b = 51.06β = 113.5
c = 60.45γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other