9JNB | pdb_00009jnb

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

PDB DOI: https://doi.org/10.2210/pdb9JNB/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.283 (Depositor), 0.285 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Dhankhar, K., Hazra, S.

To be published.

Macromolecule Content

Total Structure Weight: 29.82 kDa
Atom Count: 2,177
Modeled Residue Count: 267
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A	269	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52682
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ID1 (Subject of Investigation/LOI) Query on ID1 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Imipenem C₁₂ H₁₉ N₃ O₄ S NIJGFQHESQFJAG-ZYUZMQFOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.283 (Depositor), 0.285 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.847	α = 90
b = 50.915	β = 98.935
c = 60.835	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.