9JNC | pdb_00009jnc

Crystal Structure of SME-1 with improved electron density

• PDB DOI: https://doi.org/10.2210/pdb9JNC/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-23 Released: 2025-10-01 
• Deposition Author(s): Dhankhar, K., Hazra, S.
• Funding Organization(s): Board of Research in Nuclear Sciences (BRNS), Indian Council of Medical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of SME-1 with improved electron density

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.1 kDa 
• Atom Count: 4,203 
• Modeled Residue Count: 534 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A, B	275	Serratia marcescens	Mutation(s): 0  Gene Names: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 EC: 3.5.2.6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4 (Subject of Investigation/LOI)	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.011	α = 90
b = 51.918	β = 113.25
c = 74.925	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Dhankhar, K., Hazra, S.

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

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release