8W0P | pdb_00008w0p

BsaXI -- Type IIB R-M system

• PDB DOI: https://doi.org/10.2210/pdb8W0P/pdb
• EM Map EMD-43711: EMDB EMDataResource

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-13 Released: 2024-10-30 
• Deposition Author(s): Shen, B.W., Stoddard, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Atomic insights into the mechanism of DNA recognition and methylation by type IIB restriction-modification system: CryoEM structures of DNA free and cognate DNA bound BsaXI.

Shen, B.W., Stoddard, B.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 270.23 kDa 
• Atom Count: 19,116 
• Modeled Residue Count: 2,307 
• Deposited Residue Count: 2,308 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM.BsaXI	A, B	916	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: E5Z46_18465 EC: 2.1.1.72

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S.BsaXI	C	476	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: GT3921_04730
UniProt
Find proteins for A0A226QBA7 (Geobacillus thermocatenulatus) Explore A0A226QBA7  Go to UniProtKB:  A0A226QBA7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	D [auth A], E [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.32

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Shen, B.W., Stoddard, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM105691

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection