9YH9 | pdb_00009yh9

Crystal structure of a phage catechol 1,2-dioxygenase identified from a soil metagenomic survey

• PDB DOI: https://doi.org/10.2210/pdb9YH9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-30 Released: 2025-10-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a phage catechol 1,2-deoxygenase identified from a soil metagenomic survey.

Lovell, S., Liu, L., Buchko, G.W., Battaile, K.P., Wu, R., Cort, J.R., McClure, R., Hofmockel, K.S.

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

Macromolecule Content 

• Total Structure Weight: 41.79 kDa 
• Atom Count: 2,995 
• Modeled Residue Count: 343 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol 1,2-deoxygenase	A, B	182	metagenome	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39YH9

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.745	α = 90
b = 56.463	β = 90
c = 138.456	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Structure summary