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

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XY8

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13NG8
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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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.