9XFW | pdb_00009xfw

Crystal structure of Class A beta-lactamase BlaA in complex with Meropenem (Imine form)

PDB DOI: https://doi.org/10.2210/pdb9XFW/pdb
Entry: 9XFW supersedes: 8IY4

Classification: HYDROLASE
Organism(s): Yersinia enterocolitica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-29 Released: 2025-11-12
Deposition Author(s): Bhattachaya, S., Dhankhar, K., Hazra, S.
Funding Organization(s): Indian Council of Medical Research, Board of Research in Nuclear Sciences (BRNS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.271 (Depositor), 0.273 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Class A beta-lactamase BlaA in complex with Meropenem (Imine form)

Bhattachaya, S., Dhankhar, K., Hazra, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.45 kDa
Atom Count: 2,199
Modeled Residue Count: 260
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	294	Yersinia enterocolitica	Mutation(s): 0 Gene Names: blaA EC: 3.5.2.6
UniProt
Find proteins for Q01166 (Yersinia enterocolitica) Explore Q01166 Go to UniProtKB: Q01166
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DWZ (Subject of Investigation/LOI) Query on DWZ 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]	(2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C₁₇ H₂₇ N₃ O₅ S UUIYVKJXUXGPKB-VGWSNGFZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.271 (Depositor), 0.273 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.774	α = 90
b = 72.619	β = 94.953
c = 43.707	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: 2025-11-12

Deposition Author(s):

Bhattachaya, S.

This entry supersedes: 8IY4

Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	--
Board of Research in Nuclear Sciences (BRNS)	India	--

Revision History (Full details and data files)

Version 1.0: 2025-11-12
Type: Initial release

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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.