9DXH | pdb_00009dxh

attPmm and attBmm bound serine integrase complex in the pre-rotation state

• PDB DOI: https://doi.org/10.2210/pdb9DXH/pdb
• EM Map EMD-47288: EMDB EMDataResource
• NAKB: 9DXH

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-10-11 Released: 2026-01-21 
• Deposition Author(s): Shin, H., Rice, P.A., Olorunniji, F.J.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Basis of Directionality Control in Large Serine Integrases

Shin, H.S., Rice, P.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 324.46 kDa 
• Atom Count: 22,182 
• Modeled Residue Count: 2,372 
• Deposited Residue Count: 2,412 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Resolvase homolog YokA	A, B [auth C], G [auth I], H [auth K]	545	Bacillus subtilis	Mutation(s): 0  Gene Names: yokA, BSU21660
UniProt
Find proteins for O32006 (Bacillus subtilis (strain 168)) Explore O32006  Go to UniProtKB:  O32006

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	C [auth E], I [auth M]	34	Bacillus subtilis

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	D [auth F], J [auth N]	33	Bacillus subtilis

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	E [auth G], K [auth O]	25	Bacillus subtilis

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (24-MER)	F [auth H], L [auth P]	24	Bacillus subtilis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth A], N [auth C], O [auth I], P [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Shin, H., Rice, P.A., Olorunniji, F.J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release