6I30

Crystal structure of the AmpC from Pseudomonas aeruginosa with 1C

• PDB DOI: https://doi.org/10.2210/pdb6I30/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-02 Released: 2019-02-20 
• Deposition Author(s): Brem, J., Cahill, S.T., McDonough, M.A., Schofield, C.J.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.256 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Studies on the inhibition of AmpC and other beta-lactamases by cyclic boronates.

Cahill, S.T., Tyrrell, J.M., Navratilova, I.H., Calvopina, K., Robinson, S.W., Lohans, C.T., McDonough, M.A., Cain, R., Fishwick, C.W.G., Avison, M.B., Walsh, T.R., Schofield, C.J., Brem, J.

(2019) Biochim Biophys Acta Gen Subj 1863: 742-748

• PubMed: 30738906 
• DOI: https://doi.org/10.1016/j.bbagen.2019.02.004
• Primary Citation of Related Structures:  
  6I30


• PubMed Abstract: 
  

  The β-lactam antibiotics represent the most successful drug class for treatment of bacterial infections. Resistance to them, importantly via production of β-lactamases, which collectively are able to hydrolyse all classes of β-lactams, threatens their continued widespread use. Bicyclic boronates show potential as broad spectrum inhibitors of the mechanistically distinct serine- (SBL) and metallo- (MBL) β-lactamase families.

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Organizational Affiliation: 

Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.62 kDa 
• Atom Count: 2,752 
• Modelled Residue Count: 358 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class C beta-lactamase PDC-301	A	358	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaPDC
UniProt
Find proteins for A0A2Z4BUZ1 (Pseudomonas aeruginosa) Explore A0A2Z4BUZ1  Go to UniProtKB:  A0A2Z4BUZ1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C6S	B [auth A]	(3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid C16 H20 B N O5 ZRHUJXRVIMMHFG-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.256 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.04	α = 90
b = 75.34	β = 90
c = 100.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Brem, J., Cahill, S.T., McDonough, M.A., Schofield, C.J.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description