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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free:
0.283 (Depositor), 0.289 (DCC)
R-Value Work:
0.245 (Depositor), 0.251 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I3L4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free: 0.283 (Depositor), 0.289 (DCC)
R-Value Work: 0.245 (Depositor), 0.251 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.