6K0K

Crystal structure of Escherichia coli pyruvate kinase II

• PDB DOI: https://doi.org/10.2210/pdb6K0K/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-07 Released: 2020-05-13 
• Deposition Author(s): Zhao, C.H., Zhang, Y.P., Li, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.259 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli pyruvate kinase II

Zhao, C.H., Zhang, Y.P., Li, Y.

To be published.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 210.64 kDa 
• Atom Count: 13,318 
• Modelled Residue Count: 1,746 
• Deposited Residue Count: 1,956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D	489	Escherichia coli	Mutation(s): 0  EC: 2.7.1.40
UniProt
Find proteins for P21599 (Escherichia coli (strain K12)) Explore P21599  Go to UniProtKB:  P21599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	F [auth A], I [auth C], K [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MG	E [auth A], G [auth C], H [auth C], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.259 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.693	α = 90
b = 137.3	β = 90
c = 139.221	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Zhao, C.H., Zhang, Y.P., Li, Y.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description