9Q7Z | pdb_00009q7z

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

• PDB DOI: https://doi.org/10.2210/pdb9Q7Z/pdb
• NAKB: 9Q7Z

• 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: 3.32 Å
• R-Value Free: 
  0.286 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.244 (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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 100.8 kDa 
• Atom Count: 6,030 
• Modeled Residue Count: 682 
• Deposited Residue Count: 704 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eI-OnuI_P456_CGG	A, D	300	synthetic construct	Mutation(s): 0

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free:  0.286 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 327.795	α = 90
b = 40.472	β = 94.01
c = 78.235	γ = 90

Software Package:

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