Download MendeleyPrediction, 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.
9Q0H | pdb_00009q0h
One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence
- PDB DOI: https://doi.org/10.2210/pdb9Q0H/pdb
- NAKB: 9Q0H
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2025-08-12 Released: 2025-09-10
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.247 (Depositor), 0.252 (DCC)
- R-Value Work: 0.198 (Depositor), 0.204 (DCC)
- R-Value Observed: 0.202 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| eI-OnuI_P456_GGC_3 | 300 | synthetic construct | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (26-MER) | 26 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (26-MER) | 26 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | H [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | I [auth A], J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CA Query on CA | D [auth A] E [auth A] F [auth A] G [auth A] K [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.247 (Depositor), 0.252 (DCC)
- R-Value Work: 0.198 (Depositor), 0.204 (DCC)
- R-Value Observed: 0.202 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 39.278 | α = 90 |
| b = 75.539 | β = 90 |
| c = 167.234 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
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 |
Revision History (Full details and data files)
- Version 1.0: 2025-09-10
Type: Initial release
