9CD3 | pdb_00009cd3

Cryo-EM structure of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate

• PDB DOI: https://doi.org/10.2210/pdb9CD3/pdb
• EM Map EMD-45461: EMDB EMDataResource

• Classification: LYASE
• Organism(s): Candidatus Saccharimonadota bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2025-08-06 
• Deposition Author(s): Singal, B., Landwehr, G., Jewett, M.C.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

A synthetic pathway for cell-free upgrading of one-carbon substrates

Landwehr, G.M., Vogeli, B., Tian, C., Singal, B., Gupta, A., Lion, R., Sargent, E.H., Karim, A.S., Jewett, M.C.

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 181.46 kDa 
• Atom Count: 12,592 
• Modeled Residue Count: 1,570 
• Deposited Residue Count: 1,598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoketolase family protein	A, B	799	Candidatus Saccharimonadota bacterium	Mutation(s): 0  Gene Names: HG452_002440
UniProt
Find proteins for A0A7W4E7R7 (Candidatus Saccharibacteria bacterium) Explore A0A7W4E7R7  Go to UniProtKB:  A0A7W4E7R7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	C [auth A], D [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Singal, B., Landwehr, G., Jewett, M.C.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0023278

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release