7XM0

Crystal structure of Sau3AI-C and DNA substrate complex

• PDB DOI: https://doi.org/10.2210/pdb7XM0/pdb
• NAKB: 7XM0

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Staphylococcus aureus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-23 Released: 2023-04-26 
• Deposition Author(s): Yahui, L., Feng, Y., Jianhua, H.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

The Self-Activation Mechanism of Type IIE Restriction Endonuclease Sau3AI

Yahui, L., Feng, Y., Jianhua, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.54 kDa 
• Atom Count: 7,578 
• Modelled Residue Count: 821 
• Deposited Residue Count: 924 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II restriction enzyme Sau3AI	A, B, C	288	Staphylococcus aureus	Mutation(s): 0  Gene Names: sau3AIR EC: 3.1.21.4
UniProt
Find proteins for P16667 (Staphylococcus aureus) Explore P16667  Go to UniProtKB:  P16667

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*GP*AP*TP*CP*AP*TP*G)-3')	D, E, F, G, H, I	10	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	J [auth A], K [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.943	α = 90
b = 98.391	β = 90
c = 209.455	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Yahui, L., Feng, Y., Jianhua, H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFC2301405
National Natural Science Foundation of China (NSFC)	China	31971121
National Natural Science Foundation of China (NSFC)	China	81861138047
National Natural Science Foundation of China (NSFC)	China	U1932130

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 2.0: 2023-07-19
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Refinement description