9XY1 | pdb_00009xy1

One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence

• PDB DOI: https://doi.org/10.2210/pdb9XY1/pdb
• NAKB: 9XY1

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-25 Released: 2025-09-10 
• Deposition Author(s): Werther, R., Stoddard, B.L.
• 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: 1.92 Å
• R-Value Free: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Prediction, modeling and design of protein-DNA recognition via computational and machine learning approaches: accomplishments and remaining challenges

Esler, M.A., Werther, R., Bradley, P., Stoddard, B.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 50.97 kDa 
• Atom Count: 3,492 
• Modeled Residue Count: 345 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eI-OnuI_P456_TGA	A	300	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	B	26	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	C	26	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.671	α = 90
b = 70.44	β = 90
c = 165.936	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Werther, R., Stoddard, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM139752
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM105691
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM148166

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release