9HKY | pdb_00009hky

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

PDB DOI: https://doi.org/10.2210/pdb9HKY/pdb
EM Map EMD-52240: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM struture of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 open and 2 closed subunits

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

To be published.

Macromolecule Content

Total Structure Weight: 210.21 kDa
Atom Count: 14,148
Modeled Residue Count: 1,809
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	472	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: ahcY, sahH, PA0432 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], I [auth C], J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D]
ADN Query on ADN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	G [auth B], K [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B]	H [auth B], L [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain L [auth D] Interactions & Density Focus chain H [auth B] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419+SVN

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.