9H03 | pdb_00009h03

NMHase, dihydrouridine, 2.1A, CC_mask=0.7859

• PDB DOI: https://doi.org/10.2210/pdb9H03/pdb
• EM Map EMD-51451: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Glutamicibacter protophormiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-07 Released: 2025-10-15 
• Deposition Author(s): Toedtli, P., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche LTD

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

NMHase, dihydrouridine, 2.1A, CC_mask=0.7859

Toedtli, P., Rudolph, M.G.

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, gel filtration

Macromolecule Content 

• Total Structure Weight: 280.56 kDa 
• Atom Count: 19,564 
• Modeled Residue Count: 2,554 
• Deposited Residue Count: 2,576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-Methylhydantoinase	A, B	1,288	Glutamicibacter protophormiae	Mutation(s): 0
UniProt
Find proteins for M7MZT8 (Paeniglutamicibacter gangotriensis Lz1y) Explore M7MZT8  Go to UniProtKB:  M7MZT8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUC (Subject of Investigation/LOI)	D [auth A], F [auth B]	DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE C4 H6 N2 O2 OIVLITBTBDPEFK-UHFFFAOYSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Toedtli, P., Rudolph, M.G.

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Funding Organization	Location	Grant Number
F. Hoffmann-La Roche LTD	Switzerland	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release