Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 123.79 kDa 
• Atom Count: 8127 
• Residue Count: 1005 
• Unique protein chains: 1

5DF7

CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH AZLOCILLIN

• DOI: 10.2210/pdb5DF7/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-08-26 Released: 2016-01-13 
• Deposition Author(s): Ren, J., Nettleship, J.E., Males, A., Stuart, D.I., Owens, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms.

Ren, J., Nettleship, J.E., Males, A., Stuart, D.I., Owens, R.J.

(2016) FEBS Lett 590: 288-297

• PubMed: 26823174 
• DOI: 10.1002/1873-3468.12054
• Primary Citation of Related Structures:  
  5DF8, 5DF7, 5DF9


• PubMed Abstract: 
  

Penicillin-binding protein 3 (PBP3) from Pseudomonas aeruginosa is the molecular target of β-lactam-based antibiotics. Structures of PBP3 in complexes with azlocillin and cefoperazone, which are in clinical use for the treatment of pseudomonad infections, have been determined to 2.0 Å resolution. Together with data from other complexes, these structures identify a common set of residues involved in the binding of β-lactams to PBP3. Comparison of wild-type and an active site mutant (S294A) showed that increased thermal stability of PBP3 following azlocillin binding was entirely due to covalent binding to S294, whereas cefoperazone binding produces some increase in stability without the covalent link. Consistent with this, a third crystal structure was determined in which the hydrolysis product of cefoperazone was noncovalently bound in the active site of PBP3. This is the first structure of a complex between a penicillin-binding protein and cephalosporic acid and may be important in the design of new noncovalent PBP3 inhibitors.

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Organizational Affiliation: 

OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein	A, B	564	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names:  pbpB, ftsI_2, ERS445055_04698, PAE221_03076, YQ19_27590, ftsI, ftsI_1, ftsI_3, ALP65_00912, CAZ10_21230, CGU42_01090, DZ962_00565, E4V10_06485, ECC04_026610, F3H14_31410, F7O90_09190, F7O98_01460, FC629_25555, FDK04_24780, GNQ48_11285, HMPREF2687_22840, IPC116_09585, IPC1323_21620, IPC1481_11065, IPC1509_19770, IPC582_20545, IPC620_22215, IPC669_10550, NCTC10662_02655, NCTC12951_06549, NCTC13437_06140, NCTC13621_04221, RW109_RW109_05757 EC: 2.4.1.129 (PDB Primary Data), 3.4.16.4 (UniProt)
Find proteins for Q51504 (Pseudomonas aeruginosa) Explore Q51504  Go to UniProtKB:  Q51504

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
59H	A, B	(2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-1,3-thiazolidine-4-carboxylic acid C20 H25 N5 O6 S FATONWNMDXFMAN-HGTKMLMNSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	A, B	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.253	α = 71.26
b = 74.919	β = 85.99
c = 82.722	γ = 85.69

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-26 
• Released Date: 2016-01-13 
Deposition Author(s): Ren, J., Nettleship, J.E., Males, A., Stuart, D.I., Owens, R.J.

Revision History 

• Version 1.0: 2016-01-13
  Type: Initial release