9G4G

Staphylococcus aureus MazF in complex with Nanobody 9

• PDB DOI: https://doi.org/10.2210/pdb9G4G/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus, Lama glama
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-15 Released: 2024-07-24 
• Deposition Author(s): Zorzini, V., Haesaerts, S., Loris, R.
• Funding Organization(s): Vrije Universiteit Brussel

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.303 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

Starting Models: experimental

Literature

Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF

Prolic-Kalinsec, M., Zorzini, V., Haesaerts, S., De Bruyn, P., Loris, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.74 kDa 
• Atom Count: 1,901 
• Modelled Residue Count: 244 
• Deposited Residue Count: 267 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF	A	133	Staphylococcus aureus	Mutation(s): 0  Gene Names: mazF, SA1873 EC: 3.1
UniProt
Find proteins for Q7A4G9 (Staphylococcus aureus (strain N315)) Explore Q7A4G9  Go to UniProtKB:  Q7A4G9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 9	B	134	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.303 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.09	α = 90
b = 133.75	β = 90
c = 100.42	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Zorzini, V., Haesaerts, S., Loris, R.

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Funding Organization	Location	Grant Number
Vrije Universiteit Brussel	Belgium	SRP13

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release