8PEB

OXA-48_Q5. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution

• PDB DOI: https://doi.org/10.2210/pdb8PEB/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-06-13 Released: 2024-02-14 
• Deposition Author(s): Leiros, H.-K.S., Frohlich, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.187 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Literature

Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution.

Frohlich, C., Leiros, H.-K.S.

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: SAXS

Macromolecule Content

• Total Structure Weight: 28.41 kDa 
• Atom Count: 2,557 
• Modelled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	242	Klebsiella pneumoniae	Mutation(s): 5  Gene Names: bla OXA-48, blaOXA-48, KPE71T_00045 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0  Go to UniProtKB:  Q6XEC0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI	G [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.187 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.401	α = 90
b = 42.544	β = 106.875
c = 64.304	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Leiros, H.-K.S., Frohlich, C.

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Funding Organization	Location	Grant Number
Not funded		0000

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release