8XY8 | pdb_00008xy8

a beta-lactamase - AmpC

• PDB DOI: https://doi.org/10.2210/pdb8XY8/pdb

• Classification: HYDROLASE
• Organism(s): Paraburkholderia xenovorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-19 Released: 2025-01-22 
• Deposition Author(s): Ma, W.Z., Song, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Mechanism-Guided Protein Engineering of Paraburkholderia xenovorans Lactamase for the Green Synthesis of 2-(2-oxopyrrolidin-1-yl)-butanoic acid

Ma, W.Z., Song, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.83 kDa 
• Atom Count: 2,761 
• Modeled Residue Count: 360 
• Deposited Residue Count: 391 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	391	Paraburkholderia xenovorans	Mutation(s): 0  Gene Names: Bxe_B1593 EC: 3.5.2.6
UniProt
Find proteins for Q13NG8 (Paraburkholderia xenovorans (strain LB400)) Explore Q13NG8  Go to UniProtKB:  Q13NG8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.94	α = 90
b = 84.94	β = 90
c = 120.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Ma, W.Z., Song, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release