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

Validation slider image for 9MRI

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 K [auth D] SDF format, chain M [auth F] MOL2 format, chain K [auth D] MOL2 format, chain M [auth F] mmCIF format, chain K [auth D] mmCIF format, chain M [auth F]	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 G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain L [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth E] MOL2 format, chain N [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth E] mmCIF format, chain N [auth F]	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]

Experimental Data & Validation

Experimental Data

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)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.586	α = 90
b = 142.849	β = 90
c = 161.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Blancas Cortez, J.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5 R35GM119707-09

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.