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

Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of SME-1 with improved electron density

Dhankhar, K., Hazra, S.

To be published.

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

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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
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.280 (Depositor), 0.280 (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

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Ligand Structure Quality Assessment

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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

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