8PKB

Staphylococcus aureus endonuclease IV with bound phosphate

• PDB DOI: https://doi.org/10.2210/pdb8PKB/pdb

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


• Deposited: 2023-06-26 Released: 2024-07-10 
• Deposition Author(s): Saper, M., Kirillov, S., Rouvinski, A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Starting Model: experimental

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.56 kDa 
• Atom Count: 2,562 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
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
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.548	α = 90
b = 84.04	β = 90
c = 103.344	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Saper, M., Kirillov, S., Rouvinski, A.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

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