8XPF | pdb_00008xpf

2OG-Fe(II) oxygenase-ColD in complex with collinodins

• PDB DOI: https://doi.org/10.2210/pdb8XPF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptomyces collinus, synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-01-03 Released: 2025-01-15 
• Deposition Author(s): Zhang, B., Shi, J., Zhang, Y., Ge, H.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Biosynthesis of Collinodin Unveils Iterative Oxidative and Prenylation Modifications

Shi, J., Zhang, Y., Ren, W.Q., Shi, Y., Wei, Y.Y., Zhang, B., Jiao, R.H., Ge, H.M.

(2025) ACS Catal 15: 6628-6639

• DOI: https://doi.org/10.1021/acscatal.5c01005

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 36.73 kDa 
• Atom Count: 2,793 
• Modeled Residue Count: 301 
• Deposited Residue Count: 327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2OG-Fe(II) oxygenase	A	312	Streptomyces collinus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
small peptide	B [auth C]	15	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG (Subject of Investigation/LOI)	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	D [auth A], E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.363	α = 90
b = 61.01	β = 112.6
c = 56.346	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Zhang, B., Shi, J., Zhang, Y., Ge, H.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81925033, 22193071, 81991522, 81991524, 22107048, and 22377052
Ministry of Science and Technology (MoST, China)	China	2022YFC2804100, 2022YFC2303100, and 2018YFA0902000

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-07-30
  Changes: Database references