9IF5 | pdb_00009if5

PhiC31 S12A dimer on attB sites

• PDB DOI: https://doi.org/10.2210/pdb9IF5/pdb
• EM Map EMD-52841: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli, Streptomyces phage phi-C31
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-17 Released: 2026-03-04 
• Deposition Author(s): Spagnolo, L., Sun, Y.E., Joseph, A.P.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of DNA recombination catalysis and regulation by phiC31 integrase

Spagnolo, L., Sun, Y.E., Aspinall, L., Joseph, A.P., Stark, W.M., Colloms, S.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global 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: 132.81 kDa 
• Atom Count: 8,151 
• Modeled Residue Count: 868 
• Deposited Residue Count: 1,006 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	C [auth A], D [auth B]	450	Streptomyces phage phi-C31	Mutation(s): 0  Gene Names: int
UniProt
Find proteins for Q9T221 (Streptomyces phage phiC31) Explore Q9T221  Go to UniProtKB:  Q9T221

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (53-MER)	A [auth E]	53	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (53-MER)	B [auth F]	53	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Spagnolo, L., Sun, Y.E., Joseph, A.P.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W017571/1

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release