9PZH | pdb_00009pzh

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

• PDB DOI: https://doi.org/10.2210/pdb9PZH/pdb
• NAKB: 9PZH

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


• Deposited: 2025-08-11 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: 2.36 Å
• R-Value Free: 
  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.184 (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: 50.91 kDa 
• Atom Count: 3,608 
• Modeled Residue Count: 347 
• 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_GGC_2	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth A], E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.312	α = 90
b = 76.317	β = 90
c = 168.321	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