8IU7 | pdb_00008iu7

Structure of Staphylococcus aureus NrnA (Pde2) in complex with Mg2+

• PDB DOI: https://doi.org/10.2210/pdb8IU7/pdb

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


• Deposited: 2023-03-23 Released: 2024-04-24 
• Deposition Author(s): Cheng, K., Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: in silico

Literature

Structure of Staphylococcus aureus NrnA in complex with Mg2+.

Cheng, K., Wang, 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.15 kDa 
• Atom Count: 10,313 
• Modeled Residue Count: 1,283 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional oligoribonuclease and PAP phosphatase NrnA	A, B [auth C], C [auth D], D [auth B]	333	Staphylococcus aureus	Mutation(s): 0  Gene Names: nrnA_2 EC: 3.1
UniProt
Find proteins for A0A266CBU5 (Staphylococcus aureus) Explore A0A266CBU5  Go to UniProtKB:  A0A266CBU5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.91	α = 90
b = 119.67	β = 91.37
c = 119.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Cheng, K., Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100017
National Natural Science Foundation of China (NSFC)	China	32270043

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release