3M2K

Crystal Structure of fluorescein-labeled Class A -beta lactamase PenP in complex with cefotaxime

• PDB DOI: https://doi.org/10.2210/pdb3M2K/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-07 Released: 2011-03-16 
• Deposition Author(s): Zhao, Y.X., Leung, Y.C., Wong, W.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 

Literature

Structural studies of the mechanism for biosensing antibiotics in a fluorescein-labeled beta-lactamase.

Wong, W.T., Au, H.W., Yap, H.K., Leung, Y.C., Wong, K.Y., Zhao, Y.

(2011) BMC Struct Biol 11: 15-15

• PubMed: 21443768 
• DOI: https://doi.org/10.1186/1472-6807-11-15
• Primary Citation of Related Structures:  
  3M2K


• PubMed Abstract: 
  

  β-lactamase conjugated with environment-sensitive fluorescein molecule to residue 166 on the Ω-loop near its catalytic site is a highly effective biosensor for β-lactam antibiotics. Yet the molecular mechanism of such fluorescence-based biosensing is not well understood.

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Organizational Affiliation: 

Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.98 kDa 
• Atom Count: 3,964 
• Modelled Residue Count: 496 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	257	Bacillus licheniformis	Mutation(s): 1  Gene Names: penP EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808  Go to UniProtKB:  P00808

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEF	C [auth A], D [auth B]	CEFOTAXIME, C3' cleaved, open, bound form C14 H15 N5 O5 S2 NRYMPLKBKFIWQC-YVCCLBOHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.538	α = 90
b = 91.524	β = 104.22
c = 66.302	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Zhao, Y.X., Leung, Y.C., Wong, W.T.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Non-polymer description
• Version 2.0: 2018-09-19
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description