3UQE | pdb_00003uqe

Crystal structure of the Phosphofructokinase-2 mutant Y23D from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3UQE/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-11-20 Released: 2012-11-21 
• Deposition Author(s): Pereira, H.M., Caniuguir, A., Baez, M., Cabrera, R., Garatt, R.C., Babul, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structure of E. coli PFK2 mutant Y23D

Pereira, H.M., Caniuguir, A., Baez, M., Cabrera, R., Garratt, R.C., Babul, J.

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)

Macromolecule Content 

• Total Structure Weight: 66.34 kDa 
• Atom Count: 4,792 
• Modeled Residue Count: 612 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructokinase isozyme 2	A, B	309	Escherichia coli K-12	Mutation(s): 1  Gene Names: b1723, JW5280, PFK2, pfkB EC: 2.7.1.11
UniProt
Find proteins for P06999 (Escherichia coli (strain K12)) Explore P06999  Go to UniProtKB:  P06999

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], J [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
POP	F [auth A], H [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG	D [auth A], E [auth A], G [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.838	α = 90
b = 89.123	β = 90
c = 175.908	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Pereira, H.M., Caniuguir, A., Baez, M., Cabrera, R., Garatt, R.C., Babul, J.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description