9G2A | pdb_00009g2a

Staphylococcus aureus MazF in complex with nanobody 4

• PDB DOI: https://doi.org/10.2210/pdb9G2A/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus N315, Lama glama
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-10 Released: 2024-07-17 
• 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: 2.05 Å
• R-Value Free: 
  0.307 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Models: experimental

Literature

Staphylococcus aureus MazF in complex with nanobody 4.

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: 59.89 kDa 
• Atom Count: 3,644 
• Modeled Residue Count: 471 
• Deposited Residue Count: 534 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF	A, B	133	Staphylococcus aureus subsp. aureus N315	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 4	C, D	134	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth C], G [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MPO	F [auth C], H [auth D]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.307 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.97	α = 81.26
b = 51.65	β = 81.61
c = 70.34	γ = 71.65

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: 2024-07-17 
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: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Structure summary