9G2G | pdb_00009g2g

Staphylococcus aureus MazF in complex with nanobody 5

• PDB DOI: https://doi.org/10.2210/pdb9G2G/pdb

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


• Deposited: 2024-07-10 Released: 2024-07-24 
• Deposition Author(s): Prolic-Kalinsek, M., Zorzini, V., Haesaerts, S., Loris, R.
• Funding Organization(s): Vrije Universiteit Brussel

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Models: experimental

Literature

Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF

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: 58.68 kDa 
• Atom Count: 3,948 
• Modeled Residue Count: 476 
• Deposited Residue Count: 528 
• 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 Q2FWI8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWI8  Go to UniProtKB:  Q2FWI8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 5	C, D	131	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.6	α = 67.502
b = 50.873	β = 79.804
c = 52.083	γ = 85.349

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., 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
  
• Version 1.1: 2024-10-16
  Changes: Structure summary