9PJ2 | pdb_00009pj2

Crystal structure of non-haem diiron azetidine synthase from Streptomyces cacaoi var. asoensis complexed with iron, L-isoleucine and molecular oxygen

PDB DOI: https://doi.org/10.2210/pdb9PJ2/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:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: in silico
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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 Related Structures:
9PJ2, 9PJ3

Macromolecule Content

Total Structure Weight: 181.87 kDa
Atom Count: 13,504
Modeled Residue Count: 1,620
Deposited Residue Count: 1,650
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C1IC29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ILE (Subject of Investigation/LOI) Query on ILE Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] N [auth C] Q [auth D] S [auth E] G [auth A], J [auth B], N [auth C], Q [auth D], S [auth E], U [auth F]	ISOLEUCINE C₆ H₁₃ N O₂ AGPKZVBTJJNPAG-WHFBIAKZSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth B] K [auth B] M [auth C] O [auth C] H [auth A], I [auth B], K [auth B], M [auth C], O [auth C], R [auth D], T [auth E], V [auth F], W [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain P [auth C] SDF format, chain L [auth B] MOL2 format, chain X [auth F] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] mmCIF format, chain X [auth F] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B]	L [auth B], P [auth C], X [auth F]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth C] Focus chain X [auth F] Interactions & Density Focus chain L [auth B] Focus chain P [auth C] Focus chain X [auth F]