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

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
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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:

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

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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)

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 (Full details and data files)

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

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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.