8K3I | pdb_00008k3i

Cryo-EM structure of PseP apo

• PDB DOI: https://doi.org/10.2210/pdb8K3I/pdb
• EM Map EMD-36852: EMDB EMDataResource

• Classification: LYASE
• Organism(s): Pseudomonas fluorescens
• Expression System: Streptomyces lividans TK24
• Mutation(s): No 


• Deposited: 2023-07-15 Released: 2024-07-17 
• Deposition Author(s): Mori, T., Awakawa, T., Adachi, N., Abe, I.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of PseP apo

Mori, T., Awakawa, T., Adachi, N., Abe, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 181.9 kDa 
• Atom Count: 7,372 
• Modeled Residue Count: 960 
• Deposited Residue Count: 1,630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PseP	A, B	815	Pseudomonas fluorescens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1.3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Mori, T., Awakawa, T., Adachi, N., Abe, I.

---

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101071
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121001

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Data collection, Structure summary