4IOT | pdb_00004iot

High-resolution Structure of Triosephosphate isomerase from E. coli

• PDB DOI: https://doi.org/10.2210/pdb4IOT/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli str. K-12 substr. DH10B
• Mutation(s): No 


• Deposited: 2013-01-08 Released: 2013-01-23 
• Deposition Author(s): Vinaik, R., Kozlov, G., Gehring, K., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Triosephosphate isomerase is a common crystallization contaminant of soluble His-tagged proteins produced in Escherichia coli.

Kozlov, G., Vinaik, R., Gehring, K.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 499-502

• PubMed: 23695562 
• DOI: https://doi.org/10.1107/S1744309113010841
• Primary Citation Related Structures: 
  4IOT


• PubMed Abstract: 
  

  Attempts to crystallize several mammalian proteins overexpressed in Escherichia coli revealed a common contaminant, triosephosphate isomerase, a protein involved in glucose metabolism. Even with triosephosphate isomerase present in very small amounts, similarly shaped crystals appeared in the crystallization drops in a number of polyethylene glycol-containing conditions. All of the target proteins were His-tagged and their purification involved immobilized metal-affinity chromatography (IMAC), a step that was likely to lead to triosephosphate isomerase contamination. Analysis of the triosephosphate isomerase crystals led to the structure of E. coli triosephosphate isomerase at 1.85 Å resolution, which is a significant improvement over the previous structure.

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Organizational Affiliation: 
• Department of Biochemistry, Groupe de Recherche axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 54.1 kDa 
• Atom Count: 4,306 
• Modeled Residue Count: 508 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	255	Escherichia coli str. K-12 substr. DH10B	Mutation(s): 0  EC: 5.3.1.1
UniProt
Find proteins for B1XB85 (Escherichia coli (strain K12 / DH10B)) Explore B1XB85  Go to UniProtKB:  B1XB85

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.47	α = 90
b = 67.452	β = 90
c = 150.354	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Vinaik, R., Kozlov, G., Gehring, K., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-06-05
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description