9XBS | pdb_00009xbs

ATP-dependent diazotase Mco01_40450 binding with substrate

• PDB DOI: https://doi.org/10.2210/pdb9XBS/pdb
• EM Map EMD-66710: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Microbispora corallina
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-24 Released: 2026-08-26 
• Deposition Author(s): Ning, J., Kawai, S., Katsuyama, Y., Ohnishi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Promiscuous ATP-Dependent Diazotases Discovered by Comprehensive Genome Mining Based on Sequence Similarity Network Analysis

Ning, J., Kawai, S., Katsuyama, Y., Ohnishi, Y.

(2026) J Am Chem Soc 

• DOI: https://doi.org/10.1021/jacs.6c11480

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 63.95 kDa 
• Atom Count: 4,334 
• Modeled Residue Count: 558 
• Deposited Residue Count: 577 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty-acid-CoA ligase FadD	A	577	Microbispora corallina	Mutation(s): 0  Gene Names: Mco01_40450
UniProt
Find proteins for A0ABQ4G1Y4 (Microbispora corallina) Explore A0ABQ4G1Y4  Go to UniProtKB:  A0ABQ4G1Y4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
DPO (Subject of Investigation/LOI)	C [auth A]	DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J
AHC (Subject of Investigation/LOI)	D [auth A]	4-AMINOHYDROCINNAMIC ACID C9 H11 N O2 WXOHKMNWMKZMND-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 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: 2026-08-26 
Deposition Author(s): Ning, J., Kawai, S., Katsuyama, Y., Ohnishi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22H02192
Japan Society for the Promotion of Science (JSPS)	Japan	25K01955
Japan Society for the Promotion of Science (JSPS)	Japan	22H05130
Japan Society for the Promotion of Science (JSPS)	Japan	19H05685
Japan Society for the Promotion of Science (JSPS)	Japan	22KJ1046

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release