9XV0 | pdb_00009xv0

Crystal Structure of class C beta-lactamase PDC-16 from P.aeruginosa.

PDB DOI: https://doi.org/10.2210/pdb9XV0/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-11-25 Released: 2026-10-07
Deposition Author(s): Liji, S.S., Dhanasingh, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.312 (Depositor), 0.311 (DCC)
R-Value Work:
0.294 (Depositor), 0.294 (DCC)
R-Value Observed:
0.295 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Crystal Structure of class C beta-lactamase PDC-16 from P.aeruginosa.

Liji, S.S., Dhanasingh, I.

(2026) Int J Biol Macromol

DOI: https://doi.org/10.1016/j.ijbiomac.2026.154709

Macromolecule Content

Total Structure Weight: 78.66 kDa
Atom Count: 5,908
Modeled Residue Count: 715
Deposited Residue Count: 716
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	358	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaPDC EC: 3.5.2.6
UniProt
Find proteins for A0A1Z1VQP5 (Pseudomonas aeruginosa) Explore A0A1Z1VQP5 Go to UniProtKB: A0A1Z1VQP5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Z1VQP5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.312 (Depositor), 0.311 (DCC)
R-Value Work: 0.294 (Depositor), 0.294 (DCC)
R-Value Observed: 0.295 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.86	α = 90
b = 89.7	β = 90
c = 103.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
pointless	data scaling
iMOSFLM	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	India	--

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release