5THG | pdb_00005thg

Engineered variant of I-OnuI meganuclease targeting the HIV CCR5 gene; harbors 43 point mutations relative to wild-type I-OnuI

• PDB DOI: https://doi.org/10.2210/pdb5THG/pdb
• NAKB: 5THG

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


• Deposited: 2016-09-29 Released: 2017-05-03 
• Deposition Author(s): Hallinan, J.P., Stoddard, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Bill & Melinda Gates Foundation, bluebird bio, inc.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

The structural basis of altered gene specificity resulting from meganuclease and MegaTAL engineering

Werther, R., Hallinan, J.P., Lambert, A., Haven, K., Jarjor, J., 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: 106.29 kDa 
• Atom Count: 6,756 
• Modelled Residue Count: 698 
• Deposited Residue Count: 724 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
I-OnuI_e-hCCR5	A, D	304	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	B, E	29	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	C, F	29	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B], L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth A], H [auth A], J [auth D], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.959	α = 90
b = 112.351	β = 90
c = 122.879	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Hallinan, J.P., 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
Bill & Melinda Gates Foundation	United States	Target Malaria Program
bluebird bio, inc.	United States	Corporate Funding

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations