9GY2 | pdb_00009gy2

Non-Hemolytic Phospholipase C (PLC N)

PDB DOI: https://doi.org/10.2210/pdb9GY2/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa UCBPP-PA14
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-01 Released: 2025-10-15
Deposition Author(s): Sabharwal, N.S., Labahn, J.L.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.175 (Depositor), 0.153 (DCC)
R-Value Work:
0.152 (Depositor), 0.154 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9GY2

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

Literature

Non-Hemolytic Phospholipase C (PLC N)

Sabharwal, N.S., Labahn, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 157.93 kDa
Atom Count: 11,410
Modeled Residue Count: 1,290
Deposited Residue Count: 1,412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phospholipase C	A, B	706	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0 Gene Names: plcN, PA14_21110 EC: 3.1.4.3
UniProt
Find proteins for P15713 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P15713 Go to UniProtKB: P15713
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15713
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A, B	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.175 (Depositor), 0.153 (DCC)
R-Value Work: 0.152 (Depositor), 0.154 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.27	α = 90
b = 110.432	β = 101.03
c = 98.619	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Sabharwal, N.S.

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-10-15
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.