9HKZ | pdb_00009hkz

Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 wide open, 1 open and 1 closed subunits

• PDB DOI: https://doi.org/10.2210/pdb9HKZ/pdb
• EM Map EMD-52241: EMDB EMDataResource

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


• Deposited: 2024-12-04 Released: 2025-02-19 
• Deposition Author(s): Malecki, P.H., Wozniak, K., Ruszkowski, M., Brzezinski, K.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 wide open, 1 open and 1 closed subunits

Malecki, P.H., Wozniak, K., Ruszkowski, M., Brzezinski, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 209.86 kDa 
• Atom Count: 14,051 
• Modeled Residue Count: 1,799 
• Deposited Residue Count: 1,888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	472	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: ahcY, sahH, PA0432 EC: 3.13.2.1
UniProt
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I685  Go to UniProtKB:  Q9I685

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	I [auth D]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419+SVN

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Malecki, P.H., Wozniak, K., Ruszkowski, M., Brzezinski, K.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	SONATA BIS 2018/30/E/NZ1/00729

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release