8VMO

Homing endonuclease I-PpoI-DNA complex:ground state at pH7.0 (K+ MES) with Na+

• PDB DOI: https://doi.org/10.2210/pdb8VMO/pdb
• NAKB: 8VMO

• Classification: HYDROLASE
• Organism(s): synthetic construct, Physarum polycephalum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-13 Released: 2024-07-10 
• Deposition Author(s): Chang, C., Gao, Y.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.189 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s

Chang, C., Gao, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49 kDa 
• Atom Count: 3,784 
• Modelled Residue Count: 366 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Intron-encoded endonuclease I-PpoI	C [auth A], D [auth B]	162	Physarum polycephalum	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for Q94702 (Physarum polycephalum) Explore Q94702  Go to UniProtKB:  Q94702

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')	A [auth C], B [auth D]	21	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth C], G [auth C], K [auth A], L [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	I [auth A], J [auth A], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	E [auth C], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.189 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.083	α = 90
b = 114.083	β = 90
c = 88.123	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Chang, C., Gao, Y.

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Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR190046
Welch Foundation	United States	C-2033-20200401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008280

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release