9IOW | pdb_00009iow

Crystal Structure of SME-1 E166A Mutant in complex with Cefaclor

• PDB DOI: https://doi.org/10.2210/pdb9IOW/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-07-09 Released: 2025-07-16 
• Deposition Author(s): Dhankhar, K., Hazra, S.
• Funding Organization(s): Indian Council of Medical Research, Board of Research in Nuclear Sciences (BRNS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of SME-1 E166A Mutant in complex with Cefaclor

Dhankhar, K., Hazra, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.8 kDa 
• Atom Count: 2,126 
• Modeled Residue Count: 267 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A	275	Serratia marcescens	Mutation(s): 1  Gene Names: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 EC: 3.5.2.6
UniProt
Find proteins for P52682 (Serratia marcescens) Explore P52682  Go to UniProtKB:  P52682

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q6R (Subject of Investigation/LOI)	B [auth A]	(R)-2-((R)-((R)-2-amino-2-phenylacetamido)(carboxy)methyl)-5-chloro-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid C15 H16 Cl N3 O5 S BPKRUZRKWSLICC-SUZMYJTESA-N
CL (Subject of Investigation/LOI)	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.297	α = 90
b = 50.788	β = 98.634
c = 61.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Dhankhar, K., Hazra, S.

---

Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	EM/Dev/IG/20/773/2023
Board of Research in Nuclear Sciences (BRNS)	India	54/10/3/2023-BRNS

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release