8W2P | pdb_00008w2p

BsaXI-DNA complex I

• PDB DOI: https://doi.org/10.2210/pdb8W2P/pdb
• EM Map EMD-43754: EMDB EMDataResource
• NAKB: 8W2P

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


• Deposited: 2024-02-20 Released: 2024-10-30 
• Deposition Author(s): Shen, B.W., Stoddard, B.L., Xu, S.
• 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: 3.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI

Shen, B.W., Heiter, D., Xu, S., Stoddard, B.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 302.3 kDa 
• Atom Count: 20,780 
• Modeled Residue Count: 2,387 
• Deposited Residue Count: 2,412 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
site-specific DNA-methyltransferase (adenine-specific)	A, B	916	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: B9L19_03590 EC: 2.1.1.72
UniProt
Find proteins for A0AA91YUR9 (Geobacillus thermocatenulatus) Explore A0AA91YUR9  Go to UniProtKB:  A0AA91YUR9

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

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (41-MER) Top strand of BsaXI cognate DNA substrate	D	52	Geobacillus stearothermophilus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (41-MER) Complementary strand of BsaXI DNA substrate	E	52	Geobacillus stearothermophilus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	F [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SAH (Subject of Investigation/LOI)	H [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CA (Subject of Investigation/LOI)	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	Ro1-GM105691

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release