9BLQ | pdb_00009blq

X-ray crystal structure of Streptomyces cacaoi PolD with iron and succinate bound

• PDB DOI: https://doi.org/10.2210/pdb9BLQ/pdb

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


• Deposited: 2024-05-01 Released: 2025-11-05 
• Deposition Author(s): Collazo-Perez, L.N., Majer, S.H., Boal, A.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.261 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Mechanism and evolutionary origin of the radical-mediated C-C bond cleavage in antifungal nucleotide biosynthesis

Du, Y., Draelos, M., Collazo-Perez, L.N., Majer, S.H., Boal, A.K., Yokoyama, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.67 kDa 
• Atom Count: 3,280 
• Modeled Residue Count: 408 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydroxylase	A, B	235	Streptomyces cacaoi	Mutation(s): 0  Gene Names: polD
UniProt
Find proteins for C1IC31 (Streptomyces asoensis) Explore C1IC31  Go to UniProtKB:  C1IC31

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	E [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.261 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.828	α = 90
b = 58.828	β = 90
c = 589.086	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Collazo-Perez, L.N., Majer, S.H., Boal, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	119707

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release