3S4X | pdb_00003s4x

Crystal structure of the Asn152Gly mutant of P99 beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb3S4X/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-05-20 Released: 2012-08-01 
• Deposition Author(s): Ruble, J.F., Powers, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.234 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of the Asn152Gly mutant of P99 cephalosporinase.

Ruble, J.F., Lefurgy, S.T., Cornish, V.W., Powers, R.A.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1189-1193

• PubMed: 22948919 
• DOI: https://doi.org/10.1107/S0907444912024080
• Primary Citation Related Structures: 
  3S4X


• PubMed Abstract: 
  

  P99 cephalosporinase is a class C β-lactamase that is responsible in part for the widespread bacterial resistance to β-lactam antibiotics. Mutations of the conserved active-site residue Asn152 of the enzyme have been shown to alter β-lactam substrate specificity in vivo. Mutation of Asn152 to a glycine is notable in that it exhibits in vivo substrate-selectivity switching. In order to better understand the structural basis for this observed switch, the X-ray crystal structure of the apo Asn152Gly mutant of P99 was determined to 1.95 Å resolution. Unexpectedly, the artificial C-terminal His(6) tag of a symmetrically-related molecule was observed bound in the active site. The His(6) tag makes several interactions with key active-site residues, as well as with several sulfate ions. Additionally, the overall C-terminus occupies the space left vacant upon the mutation of Asn152 to glycine.

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Organizational Affiliation: 
• Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.75 kDa 
• Atom Count: 3,072 
• Modeled Residue Count: 367 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	367	Enterobacter cloacae	Mutation(s): 4  Gene Names: ampC EC: 3.5.2.6
UniProt
Find proteins for P05364 (Enterobacter cloacae) Explore P05364  Go to UniProtKB:  P05364

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.234 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.956	α = 90
b = 85.481	β = 90
c = 51.681	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Ruble, J.F., Powers, R.A.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2013-01-23
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description