9NLO | pdb_00009nlo

Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9NLO/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-03-03 Released: 2025-11-19 
• Deposition Author(s): Paetzel, M., Luo, C.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.213 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli type I signal peptidase P84A in complex with lipopeptide antibiotic arylomycin A2

Luo, C., Paetzel, M.

(2025) J Struct Biol : 108260

• DOI: https://doi.org/10.1016/j.jsb.2025.108260

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.7 kDa 
• Atom Count: 3,726 
• Modeled Residue Count: 467 
• Deposited Residue Count: 510 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase I	A, B	249	Escherichia coli K-12	Mutation(s): 1  Gene Names: lepB, b2568, JW2552 EC: 3.4.21.89
UniProt
Find proteins for P00803 (Escherichia coli (strain K12)) Explore P00803  Go to UniProtKB:  P00803

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARYLOMYCIN A2	C, D	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M12 (Subject of Investigation/LOI)	G [auth C], H [auth D]	10-METHYLUNDECANOIC ACID C12 H24 O2 QJRRBVNPIKYRQJ-UHFFFAOYSA-N
EDO	E [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5PG	C, D	L-PEPTIDE LINKING	C9 H11 N O3		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000117	C, D	ARYLOMYCIN A2	Lipopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.213 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.8	α = 90
b = 71.8	β = 90
c = 263.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Paetzel, M., Luo, C.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release