4XXR

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)

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

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

PubMed: 25753149 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L5C7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JSE Query on JSE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
JSC Query on JSC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	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		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth B]
JSD Query on JSD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	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		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

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 = 44.899	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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Lewandowski, E.M.

Chen, Y.

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