9IVL | pdb_00009ivl

Crystal Structure of SME-1 E166A mutant in complex with Biapenem

• PDB DOI: https://doi.org/10.2210/pdb9IVL/pdb

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


• Deposited: 2024-07-23 Released: 2025-07-30 
• Deposition Author(s): Dhankhar, K., Hazra, S.
• Funding Organization(s): Indian Council of Medical Research, Board of Research in Nuclear Sciences (BRNS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.177 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of SME-1 E166A mutant in complex with Biapenem

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: 30.83 kDa 
• Atom Count: 2,344 
• Modeled Residue Count: 265 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMG	C [auth A]	(4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate C15 H20 N4 O4 S FXUMZXFCLFWWAR-CNVPUSNMSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.177 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.605	α = 90
b = 51.728	β = 90
c = 88.226	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: 2025-07-30 
Deposition Author(s): Dhankhar, K., Hazra, S.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	EM/Dev/IG/20/0773/2023
Board of Research in Nuclear Sciences (BRNS)	India	54/14/03/2023-BRNS

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release