7RCD | pdb_00007rcd

Second stage reengineered variant of I-OnuI targeting human PD1 gene with activity enhancing substitutions

• PDB DOI: https://doi.org/10.2210/pdb7RCD/pdb
• NAKB: 7RCD

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


• Deposited: 2021-07-07 Released: 2022-06-29 
• Deposition Author(s): Ubilla-Rodriguez, N.C., Werther, R.A., Stoddard, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Characterization 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.

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: 51.05 kDa 
• Atom Count: 3,250 
• Modelled Residue Count: 339 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
I-OnuI_e-hPD1-c	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.614	α = 90
b = 64.457	β = 90
c = 169.913	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Ubilla-Rodriguez, N.C., Werther, R.A., 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	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  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description