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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9H03

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

Literature

NMHase, dihydrouridine, 2.1A, CC_mask=0.7859

Toedtli, P., Rudolph, M.G.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M7MZT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DUC (Subject of Investigation/LOI) Query on DUC Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE C₄ H₆ N₂ O₂ OIVLITBTBDPEFK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-15
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.