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 3V3S | pdb_00003v3s

Crystal structure of GES-18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.196 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

GES-18, a new carbapenem-hydrolyzing GES-Type beta-lactamase from pseudomonas aeruginosa that contains Ile80 and Ser170 residues.

Bebrone, C., Bogaerts, P., Delbruck, H., Bennink, S., Kupper, M.B., Rezende de Castro, R., Glupczynski, Y., Hoffmann, K.M.

(2013) Antimicrob Agents Chemother 57: 396-401

  • DOI: https://doi.org/10.1128/AAC.01784-12
  • Primary Citation Related Structures: 
    3V3S

  • PubMed Abstract: 

    A clinical isolate of Pseudomonas aeruginosa recovered from the lower respiratory tract of an 81-year-old patient hospitalized in Belgium was sent to the national reference center to determine its resistance mechanism. PCR sequencing identified a new GES variant, GES-18, which differs from the carbapenem-hydrolyzing enzyme GES-5 by a single amino acid substitution (Val80Ile, in the numbering according to Ambler) and from GES-1 by two substitutions (Val80Ile and Gly170Ser). Detailed kinetic characterization showed that GES-18 and GES-5 hydrolyze imipenem and cefoxitin with similar kinetic parameters and that GES-18 was less susceptible than GES-1 to classical β-lactamase inhibitors such as clavulanate and tazobactam. The overall structure of GES-18 is similar to the solved structures of GES-1 and GES-2, the Val80Ile and Gly170Ser substitutions causing only subtle local rearrangements. Notably, the hydrolytic water molecule and the Glu166 residue were slightly displaced compared to their counterparts in GES-1. Our kinetic and crystallographic data for GES-18 highlight the pivotal role of the Gly170Ser substitution which distinguishes GES-5 and GES-18 from GES-1.


  • Organizational Affiliation: 
    • Institute of Molecular Biotechnology, RWTH-Aachen University, c/o Fraunhofer IME, Aachen, Germany. carine.bebrone@molbiotech

Macromolecule Content 

  • Total Structure Weight: 62.47 kDa 
  • Atom Count: 4,741 
  • Modeled Residue Count: 537 
  • Deposited Residue Count: 574 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Extended spectrum beta-lactamase GES-18
A, B
287Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaGes
EC: 3.5.2.6
UniProt
Find proteins for H2ERK4 (Pseudomonas aeruginosa)
Explore H2ERK4 
Go to UniProtKB:  H2ERK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2ERK4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.196 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.184α = 90
b = 80.506β = 90
c = 87.748γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary