6FM7 | pdb_00006fm7

Crystal structure of the class C beta-lactamase TRU-1 from Aeromonas enteropelogenes in complex with avibactam

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 
    0.136 (Depositor), 0.136 (DCC) 
  • R-Value Work: 
    0.116 (Depositor), 0.116 (DCC) 
  • R-Value Observed: 
    0.117 (Depositor) 

Starting Model: experimental
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Literature

Atomic-Resolution Structure of a Class C beta-Lactamase and Its Complex with Avibactam.

Pozzi, C., Di Pisa, F., De Luca, F., Benvenuti, M., Docquier, J.D., Mangani, S.

(2018) ChemMedChem 13: 1437-1446

  • DOI: https://doi.org/10.1002/cmdc.201800213
  • Primary Citation Related Structures: 
    6FM6, 6FM7

  • PubMed Abstract: 

    β-Lactamases (BLs) are important antibiotic-resistance determinants that significantly compromise the efficacy of valuable β-lactam antibacterial drugs. Thus, combinations with BL inhibitor were developed. Avibactam is the first non-β-lactam BL inhibitor introduced into clinical practice. Ceftazidime-avibactam represents one of the few last-resort antibiotics available for the treatment of infections caused by near-pandrug-resistant bacteria. TRU-1 is a chromosomally encoded AmpC-type BL of Aeromonas enteropelogenes, related to the FOX-type BLs and constitutes a good model for class C BLs. TRU-1 crystals provided ultrahigh-resolution diffraction data for the native enzyme and for its complex with avibactam. A comparison of the native and avibactam-bound structures revealed new details in the conformations of residues relevant for substrate and/or inhibitor binding. Furthermore, a comparison of the TRU-1 and Pseudomonas aeruginosa AmpC avibactam-bound structures revealed two inhibitor conformations that were likely to correspond to two different states occurring during inhibitor carbamylation/recyclization.

    • Organizational Affiliation: 
    • Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy.

Macromolecule Content 

  • Total Structure Weight: 42.41 kDa 
  • Atom Count: 3,470 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 382 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase382Aeromonas enteropelogenesMutation(s): 0 
Gene Names: ampC
EC: 3.5.2.6
UniProt
Find proteins for A0A175VLQ4 (Aeromonas enteropelogenes)
Explore A0A175VLQ4 
Go to UniProtKB:  A0A175VLQ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A175VLQ4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free:  0.136 (Depositor), 0.136 (DCC) 
  • R-Value Work:  0.116 (Depositor), 0.116 (DCC) 
  • R-Value Observed: 0.117 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.552α = 90
b = 78.248β = 106.54
c = 48.306γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Structure summary