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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9JNB

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.