6BDA | pdb_00006bda

Wild-type I-OnuI bound to A3G substrate (post-cleavage complex)

• PDB DOI: https://doi.org/10.2210/pdb6BDA/pdb
• NAKB: 6BDA

• Classification: HYDROLASE/DNA
• Organism(s): Ophiostoma novo-ulmi subsp. americana, Ophiostoma novo-ulmi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-22 Released: 2018-10-24 
• Deposition Author(s): Brown, C., Zhang, K., Laforet, M., McMurrough, T., Gloor, G.B., Edgell, D.R., Junop, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Wild-type I-OnuI bound to A3G substrate (post-cleavage complex)

Laforet, M., McMurrough, T., Brown, C., Zhang, K., Junop, M., Gloor, G.B., Edgell, D.R.

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: 50.6 kDa 
• Atom Count: 3,864 
• Modeled Residue Count: 345 
• Deposited Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein 3/homing endonuclease-like protein fusion	A	307	Ophiostoma novo-ulmi subsp. americana	Mutation(s): 0  Gene Names: HEG fusion, rps3
UniProt
Find proteins for Q4VWW5 (Ophiostoma novo-ulmi subsp. americana) Explore Q4VWW5  Go to UniProtKB:  Q4VWW5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Cleaved Cognate DNA strand, +11 sense	B	14	Ophiostoma novo-ulmi

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Cleaved cognate DNA strand, -11 sense	C	11	Ophiostoma novo-ulmi

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Cleaved cognate DNA strand, -11 antisense	D	15	Ophiostoma novo-ulmi

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Cleaved cognate DNA strand, +11 antisense	E	10	Ophiostoma novo-ulmi

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.69	α = 90
b = 68.98	β = 90
c = 161.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Brown, C., Zhang, K., Laforet, M., McMurrough, T., Gloor, G.B., Edgell, D.R., Junop, M.

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations