9KRT | pdb_00009krt

E. coli MaeB holo form

• PDB DOI: https://doi.org/10.2210/pdb9KRT/pdb
• EM Map EMD-62540: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-28 Released: 2025-12-03 
• Deposition Author(s): Sassa, M., Yamato, H., Tanino, H., Fukuda, Y., Inoue, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Malic enzymes from different bacteria evolved distinct effector binding sites showing the same allosteric regulation mechanism

Sassa, M., Yamato, H., Tanino, H., Fukuda, Y., Inoue, T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.27 kDa 
• Atom Count: 5,822 
• Modeled Residue Count: 758 
• Deposited Residue Count: 759 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent malic enzyme	A	759	Escherichia coli K-12	Mutation(s): 0  Gene Names: maeB, ypfF, b2463, JW2447 EC: 1.1.1.40
UniProt
Find proteins for P76558 (Escherichia coli (strain K12)) Explore P76558  Go to UniProtKB:  P76558

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Sassa, M., Yamato, H., Tanino, H., Fukuda, Y., Inoue, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release