8AXY

Staphylococcus aureus endonuclease IV orthorhombic crystal form

• PDB DOI: https://doi.org/10.2210/pdb8AXY/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-01 Released: 2023-09-13 
• Deposition Author(s): Rouvinski, A., Kirillov, S., Saper, M.A., Wiener, R., Isupov, M.N.
• Funding Organization(s): Jacob and Lena Joels Memorial Foundation, Hebrew University of Jerusalem, Ministry of Education and Science of the Republic of Kazakhstan

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.158 
• R-Value Work: 0.136 

Literature

Octahedrally coordinated iron in the catalytic site of endonuclease IV from Staphylococcus aureus

Kirillov, S., Isupov, M.N., Paterson, N., Wiener, R., Abeldenov, S., Saper, M.A., Rouvinski, A.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.55 kDa 
• Atom Count: 3,153 
• Modelled Residue Count: 296 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable endonuclease 4	A	296	Staphylococcus aureus	Mutation(s): 0  Gene Names: nfo, SAR1634 EC: 3.1.21.2
UniProt
Find proteins for Q6GGE2 (Staphylococcus aureus (strain MRSA252)) Explore Q6GGE2  Go to UniProtKB:  Q6GGE2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.158 
• R-Value Work: 0.136 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.857	α = 90
b = 82.581	β = 90
c = 105.091	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MoRDa	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Rouvinski, A., Kirillov, S., Saper, M.A., Wiener, R., Isupov, M.N.

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Funding Organization	Location	Grant Number
Jacob and Lena Joels Memorial Foundation, Hebrew University of Jerusalem	Israel	--
Ministry of Education and Science of the Republic of Kazakhstan	Kazakhstan	AP08856811

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release