8EDQ | pdb_00008edq

E. coli pyruvate kinase (PykF) I264F

PDB DOI: https://doi.org/10.2210/pdb8EDQ/pdb

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

Deposited: 2022-09-05 Released: 2022-11-16
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: 2.88 Å
R-Value Free:
0.241 (Depositor), 0.187 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 102.13 kDa
Atom Count: 7,029
Modeled Residue Count: 927
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B	470	Escherichia coli	Mutation(s): 1 Gene Names: pykF EC: 2.7.1.40
UniProt
Find proteins for P0AD61 (Escherichia coli (strain K12)) Explore P0AD61 Go to UniProtKB: P0AD61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AD61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.241 (Depositor), 0.187 (DCC)
R-Value Work: 0.202 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.87	α = 90
b = 244.931	β = 90
c = 134.284	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2023-10-18
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.