5UJO | pdb_00005ujo

X-Ray Crystal Structure of Ruthenocenyl-7-Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with CTX-M-14 E166A Beta-Lactamase

  • Classification: HYDROLASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-01-18 Released: 2017-02-08 
  • Deposition Author(s): Lewandowski, E.M., Chen, Y.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Polish National Science Centre

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.150 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.125 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.127 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

Antibacterial Properties of Metallocenyl-7-ADCA Derivatives and Structure in Complex with CTX-Mbeta-Lactamase.

Lewandowski, E.M.Szczupak, L.Wong, S.Skiba, J.Guspiel, A.Solecka, J.Vrcek, V.Kowalski, K.Chen, Y.

(2017) Organometallics 36: 1673-1676

  • DOI: https://doi.org/10.1021/acs.organomet.6b00888
  • Primary Citation Related Structures: 
    5UJO

  • PubMed Abstract: 

    A series of six novel metallocenyl-7-ADCA (metallocenyl = ferrocenyl or ruthenocenyl; 7-ADCA = 7-aminodesacetoxycephalosporanic acid) conjugates were synthesized and their antibacterial properties evaluated by biochemical and microbiological assays. The ruthenocene derivatives showed a higher level of inhibition of DD-carboxypeptidase 64-575, a Penicillin Binding Protein (PBP), than the ferrocene derivatives and the reference compound penicillin G. Protein X-ray crystallographic analysis revealed a covalent acyl-enzyme complex of a ruthenocenyl compound with CTX-M β-lactamase E166A mutant, corresponding to a similar complex with PBPs responsible for the bactericidal activities of these compounds. Most interestingly, an intact compound was captured at the crystal-packing interface, elucidating for the first time the structure of a metallocenyl β-lactam compound that previously eluded small molecule crystallography. We propose that protein crystals, even from biologically unrelated molecules, can be utilized to determine structures of small molecules.


  • Organizational Affiliation
    • Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States.

Macromolecule Content 

  • Total Structure Weight: 58.09 kDa 
  • Atom Count: 5,029 
  • Modeled Residue Count: 522 
  • Deposited Residue Count: 526 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
263Escherichia coliMutation(s): 1 
Gene Names: blaCTX-MCTX-M-14
EC: 3.5.2.6
UniProt
Find proteins for Q9L5C8 (Escherichia coli)
Explore Q9L5C8 
Go to UniProtKB:  Q9L5C8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8CY

Query on 8CY



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
ruthenocenyl-7-aminodesacetoxycephalosporanic acid, bound form
C22 H15 N2 O6 Ru S
RODYUOCEXNRXSR-FZMMWMHASA-N
LSI

Query on LSI



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
ruthenocenyl-7-aminodesacetoxycephalosporanic acid
C22 H22 N2 O5 Ru S
VVYXHQVDQWFSGH-DRUSRECESA-N
K

Query on K



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.150 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.125 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.127 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.961α = 90
b = 107.351β = 101.36
c = 47.956γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI03158
Polish National Science CentrePolandDEC-2013/11/B/ST5/00997

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-10-23
    Changes: Structure summary