7OO1 | pdb_00007oo1

Structure, function and characterization of a second pyruvate kinase isozyme in Pseudomonas aeruginosa.

• PDB DOI: https://doi.org/10.2210/pdb7OO1/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-26 Released: 2021-11-03 
• Deposition Author(s): Abdelhamid, Y., Wang, M., Parkhill, S., Brear, P., Welch, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Yousef Jameel Scholarship, Cystic Fibrosis Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: in silico

Literature

Structure, Function and Regulation of a Second Pyruvate Kinase Isozyme in Pseudomonas aeruginosa

Abdelhamid, Y., Wang, M., Parkhill, S.L., Brear, P., Chee, X., Rahman, T., Welch, M.

(2021) Front Microbiol 12: 3535

• DOI: https://doi.org/10.3389/fmicb.2021.790742

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 103.21 kDa 
• Atom Count: 7,212 
• Modeled Residue Count: 951 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B	477	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pykF, PA1498 EC: 2.7.1.40
UniProt
Find proteins for Q9I3L4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I3L4  Go to UniProtKB:  Q9I3L4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.049	α = 90
b = 169.049	β = 90
c = 115.106	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Abdelhamid, Y., Wang, M., Parkhill, S., Brear, P., Welch, M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M019411/1
Yousef Jameel Scholarship		--
Cystic Fibrosis Foundation	United Kingdom	SRC017

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2021-11-24
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Refinement description