9MRI | pdb_00009mri

X-ray crystal structure of Streptomyces cacaoi PolF bound to Zn(II)

PDB DOI: https://doi.org/10.2210/pdb9MRI/pdb

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

Deposited: 2025-01-08 Released: 2025-10-22
Deposition Author(s): Blancas Cortez, J.J., Boal, A.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Radical-dependent azetidine biosynthesis by a diiron enzyme

Du, Y., Thanapipatsiri, A., Salas Sola, X.E., Blancas Cortez, J.J., Lin, C.Y., Boal, A.K., Krebs, C., Bollinger, J.M., Yokoyama, K.

To be published.

Macromolecule Content

Total Structure Weight: 194.09 kDa
Atom Count: 12,651
Modeled Residue Count: 1,590
Deposited Residue Count: 1,770
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-bound non-heme metalloenzyme	A, B, C, D, E A, B, C, D, E, F	295	Streptomyces cacaoi	Mutation(s): 0
UniProt
Find proteins for A0ABQ3RYD4 (Streptomyces asoensis) Explore A0ABQ3RYD4 Go to UniProtKB: A0ABQ3RYD4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0ABQ3RYD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain K [auth D] MOL2 format, chain M [auth F] MOL2 format, chain K [auth D] mmCIF format, chain M [auth F] mmCIF format, chain K [auth D]	K [auth D], M [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain M [auth F] Interactions & Density Focus chain K [auth D] Focus chain M [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain L [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth F] MOL2 format, chain L [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth F] mmCIF format, chain L [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] L [auth E] G [auth A], H [auth B], I [auth C], J [auth D], L [auth E], N [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Focus chain N [auth F]