8EQ1

Escherichia coli pyruvate kinase D127N

• PDB DOI: https://doi.org/10.2210/pdb8EQ1/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-10-07 Released: 2023-01-18 
• Deposition Author(s): Donovan, K.A., Coombes, D., Dobson, R.C.J., Cooper, T.F.
• Funding Organization(s): Other government, National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.224 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Beneficial mutations occurring in E. coli pyruvate kinase afford new allosteric mechanisms leading to faster resumption of growth

Donovan, K.A., Coombes, D., Dobson, R.C.J., Cooper, T.F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 203.55 kDa 
• Atom Count: 13,992 
• Modelled Residue Count: 1,856 
• Deposited Residue Count: 1,880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B [auth C], C [auth B], D	470	Escherichia coli	Mutation(s): 1  Gene Names: EL79_2019, EL80_2048 EC: 2.7.1.40
UniProt
Find proteins for P0AD61 (Escherichia coli (strain K12)) Explore P0AD61  Go to UniProtKB:  P0AD61

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.224 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.26	α = 90
b = 131.755	β = 107.18
c = 129.091	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Donovan, K.A., Coombes, D., Dobson, R.C.J., Cooper, T.F.

---

Funding Organization	Location	Grant Number
Other government		US Army Research Office W911NF-11-1-0481
National Science Foundation (NSF, United States)	United States	DEB-1253650

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description