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
View more details

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: 181.87 kDa
Atom Count: 13,504
Modeled Residue Count: 1,620
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 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 G [auth A] SDF format, chain N [auth C] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth B]	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 H [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain R [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B]	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 L [auth B] SDF format, chain P [auth C] SDF format, chain X [auth F] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain X [auth F] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain X [auth F]	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]