9HKJ | pdb_00009hkj

Structure of Formosin D

• PDB DOI: https://doi.org/10.2210/pdb9HKJ/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Bacillus licheniformis DSM 13 = ATCC 14580
• Mutation(s): No 


• Deposited: 2024-12-03 Released: 2025-12-17 
• Deposition Author(s): Palm, G.J., Lammers, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.153 (DCC) 

Starting Model: in silico

Literature

A highly expressed antimicrobial protein produced by Bacillus licheniformis

Hilkmann, A., Palm, G.J., Lammers, M., Schweder, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 9.91 kDa 
• Atom Count: 821 
• Modeled Residue Count: 85 
• Deposited Residue Count: 85 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactococcin 972 family bacteriocin	A	85	Bacillus licheniformis DSM 13 = ATCC 14580	Mutation(s): 0
UniProt
Find proteins for Q65CU4 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65CU4  Go to UniProtKB:  Q65CU4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A], C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.153 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 21.02	α = 90
b = 41.803	β = 96.609
c = 46.758	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Palm, G.J., Lammers, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release