9PJ3 | pdb_00009pj3

Crystal structure of Non-haem Diiron Azetidine Synthase from Streptomyces cacaoi var. asoensis complexed with manganese and (R)-2-amino-3-methylbut-3-enoic acid

PDB DOI: https://doi.org/10.2210/pdb9PJ3/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptomyces cacaoi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-11 Released: 2025-12-24
Deposition Author(s): Shen, Y., Zheng, Y.-C., Chang, W.-c.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Correction to "Discovery and Mechanism of a Diiron Enzyme in Ethylidene Azetidine Formation".

Shen, Y., Zheng, Y.C., Palacios, P.M., Wang, K., Maggiolo, A.O., Guo, Y., Chang, W.C.

(2025) J Am Chem Soc 147: 43198-43198

PubMed: 41190445 Search on PubMed
DOI: https://doi.org/10.1021/jacs.5c18214
Primary Citation of Related Structures:
9PJ2, 9PJ3

Macromolecule Content

Total Structure Weight: 181.51 kDa
Atom Count: 13,304
Modeled Residue Count: 1,614
Deposited Residue Count: 1,650
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative molybdopterin oxidoreductase	A, B, C, D, E A, B, C, D, E, F	275	Streptomyces cacaoi	Mutation(s): 0 Gene Names: polF
UniProt
Find proteins for C1IC29 (Streptomyces asoensis) Explore C1IC29 Go to UniProtKB: C1IC29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1IC29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CIL (Subject of Investigation/LOI) Query on A1CIL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F]	H [auth A] I [auth B] L [auth C] N [auth D] P [auth E] H [auth A], I [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	(2R)-2-amino-3-methylbut-3-enoic acid C₅ H₉ N O₂ CJNBBWGXTPGZRW-SCSAIBSYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	G [auth A] J [auth B] K [auth C] M [auth D] O [auth E] G [auth A], J [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]