9GL1

Crystal Structure of Acetylpolyamine aminohydrolase (ApaH) from Legionella cherrii

• PDB DOI: https://doi.org/10.2210/pdb9GL1/pdb

• Classification: HYDROLASE
• Organism(s): Legionella cherrii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-26 Released: 2024-11-06 
• Deposition Author(s): Graf, L.G., Schulze, S., Palm, G.J., Lammers, M.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.266 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Starting Model: in silico

Literature

Distribution and diversity of classical deacylases in bacteria

Graf, L.G., Moreno-Yruela, C., Qin, C., Schulze, S., Palm, G.J., Schmoeker, O., Wang, N., Hocking, D., Jebeli, L., Girbardt, B., Berndt, L., Weis, D.M., Janetzky, M., Zuehlke, D., Sievers, S., Strugnell, R.A., Olsen, C.A., Hofmann, K., Lammers, M.

(2024) Nature Communications 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 46.28 kDa 
• Atom Count: 3,141 
• Modelled Residue Count: 389 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylpolyamine aminohydrolase	A	402	Legionella cherrii	Mutation(s): 0  Gene Names: bcp, Lche_0649
UniProt
Find proteins for A0A0W0SGS1 (Legionella cherrii) Explore A0A0W0SGS1  Go to UniProtKB:  A0A0W0SGS1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.266 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.564	α = 90
b = 113.564	β = 90
c = 90.426	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Graf, L.G., Schulze, S., Palm, G.J., Lammers, M.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	LA2984/6-1
German Research Foundation (DFG)	Germany	LA2984/8-1

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release