4XXR

Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with CTX-M-14 E166A Beta-Lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Antibacterial properties and atomic resolution X-ray complex crystal structure of a ruthenocene conjugated beta-lactam antibiotic.

Lewandowski, E.M.Skiba, J.Torelli, N.J.Rajnisz, A.Solecka, J.Kowalski, K.Chen, Y.

(2015) Chem Commun (Camb) 51: 6186-6189

  • DOI: https://doi.org/10.1039/c5cc00904a
  • Primary Citation of Related Structures:  
    4XXR

  • PubMed Abstract: 

    We have determined a 1.18 Å resolution X-ray crystal structure of a novel ruthenocenyle-6-aminopenicillinic acid in complex with CTX-M β-lactamase, showing unprecedented details of interactions between ruthenocene and protein. As the first product complex with an intact catalytic serine, the structure also offers insights into β-lactamase catalysis and inhibitor design.


  • Organizational Affiliation

    Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, USA. ychen1@health.usf.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTX-M-14 Class A Beta-Lactamase
A, B
263Escherichia coliMutation(s): 1 
Gene Names: 
EC: 3.5.2.6
UniProt
Find proteins for Q9L5C7 (Escherichia coli)
Explore Q9L5C7 
Go to UniProtKB:  Q9L5C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JSE
Query on JSE

Download Ideal Coordinates CCD File 
F [auth A][(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium
C22 H17 N2 O6 Ru S
DONWCTWXNJLLEK-PAALKQLMSA-N
JSC
Query on JSC

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
J [auth B]
[(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium
C22 H17 N2 O6 Ru S
DONWCTWXNJLLEK-HTTVLNLHSA-N
JSD
Query on JSD

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
[(1,2,3,4,5-eta)-1-(4-{[(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium
C21 H17 N2 O4 Ru S
JRWKHIBMJXULTB-BQFBZIMZSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.899α = 90
b = 106.775β = 101.87
c = 47.903γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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 StatesAI 103158

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2016-03-09
    Changes: Experimental preparation
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description