Download MendeleyCharacterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease
Werther, R.A., Ubilla-Rodriguez, N.C., Smiley, A.T., Havens, K., Lambert, A.R., Stoddard, B.L.To be published.
7RCF
Fourth stage reengineered variant of I-OnuI with stability enhancing substitutions
- PDB DOI: https://doi.org/10.2210/pdb7RCF/pdb
- NAKB: 7RCF
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2021-07-07 Released: 2022-06-29
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.23 Å
- R-Value Free: 0.229
- R-Value Work: 0.190
- R-Value Observed: 0.193
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| I-OnuI_e-hPD1-e | 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 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | D [auth A], E [auth A], K [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth A], G [auth A], H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | I [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | J [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.23 Å
- R-Value Free: 0.229
- R-Value Work: 0.190
- R-Value Observed: 0.193
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 41.55 | α = 90 |
| b = 64.055 | β = 90 |
| c = 171.296 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| HKL-2000 | data processing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-06-29 Deposition Author(s): Ubilla-Rodriguez, N.C., Werther, R.A., Stoddard, B.L.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | NIH R01 GM105691 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | NIH R01 GM 139752 |
| Other private | United States | Funding from bluebird bio |
Revision History (Full details and data files)
- Version 1.0: 2022-06-29
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
