5DLO | pdb_00005dlo

S. aureus MazF in complex with substrate analogue

• PDB DOI: https://doi.org/10.2210/pdb5DLO/pdb
• NAKB: 5DLO

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus, Escherichia phage MS2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-07 Released: 2016-09-28 
• Deposition Author(s): Zorzini, V., Loris, R.
• Funding Organization(s): Fonds Wetenschappelijk Onderzoek

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.163 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Substrate recognition, regulation mechanism and activity regulation of MazF mRNA interferase.

Zorzini, V., Loris, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.07 kDa 
• Atom Count: 1,213 
• Modeled Residue Count: 122 
• Deposited Residue Count: 140 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

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 Q2FWI8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWI8  Go to UniProtKB:  Q2FWI8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA substrate analogue AUACAUA	B	7	Escherichia phage MS2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.163 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.6	α = 90
b = 63.6	β = 90
c = 69.76	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Zorzini, V., Loris, R.

---

Funding Organization	Location	Grant Number
Fonds Wetenschappelijk Onderzoek	Belgium	--

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Derived calculations
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-07-24
  Changes: Database references, Source and taxonomy, Structure summary