9G5Z

Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF

• PDB DOI: https://doi.org/10.2210/pdb9G5Z/pdb

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


• Deposited: 2024-07-17 Released: 2024-07-24 
• Deposition Author(s): Prolic-Kalinsek, M., Haesaerts, S., Loris, R.
• Funding Organization(s): Vrije Universiteit Brussel

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 0.283 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Starting Models: experimental

Literature

Staphylococcus aureus MazF in complex with Nanobody 11

Prolic-Kalinsek, 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: 57.54 kDa 
• Atom Count: 3,448 
• Modelled Residue Count: 460 
• Deposited Residue Count: 514 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF	A, B	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 11	C, D	124	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 0.283 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.1	α = 90
b = 102.1	β = 90
c = 101.15	γ = 120

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): Prolic-Kalinsek, M., 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