9PZ7 | pdb_00009pz7

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

PDB DOI: https://doi.org/10.2210/pdb9PZ7/pdb
NAKB: 9PZ7

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

Deposited: 2025-08-08 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

Total Structure Weight: 50.97 kDa
Atom Count: 3,438
Modeled Residue Count: 346
Deposited Residue Count: 352
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eI-OnuI_P456_TCA	A	300	synthetic construct	Mutation(s): 0

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (26-MER)	B	26	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (26-MER)	C	26	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A]	F [auth A], H [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.208	α = 90
b = 63.739	β = 90
c = 166.752	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

View Full Validation Report

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Werther, R.

Stoddard, B.L.

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