4XXR | pdb_00004xxr

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

• PDB DOI: https://doi.org/10.2210/pdb4XXR/pdb

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


• Deposited: 2015-01-30 Released: 2015-03-18 
• Deposition Author(s): Lewandowski, E.M., Chen, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.153 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

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

• PubMed: 25753149 
• DOI: https://doi.org/10.1039/c5cc00904a
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.11 kDa 
• Atom Count: 5,221 
• Modeled Residue Count: 522 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTX-M-14 Class A Beta-Lactamase	A, B	263	Escherichia coli	Mutation(s): 1  Gene Names:  blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, ETN48_p0088, pCT_085, pHK01_011 EC: 3.5.2.6
UniProt
Find proteins for Q9L5C7 (Escherichia coli) Explore Q9L5C7  Go to UniProtKB:  Q9L5C7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JSE	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	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	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	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 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.899	α = 90
b = 106.775	β = 101.87
c = 47.903	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Lewandowski, E.M., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI 103158

Revision History  

• 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