9IUB | pdb_00009iub

Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)

PDB DOI: https://doi.org/10.2210/pdb9IUB/pdb
EM Map EMD-60896: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Mycolicibacterium smegmatis, Mycobacterium phage Bxb1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-07-20 Released: 2026-03-04
Deposition Author(s): Soma, T., Hiraizumi, M., Yamashita, K., Nishimasu, H.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.08 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)

Soma, T.

To be published.

Macromolecule Content

Total Structure Weight: 70.62 kDa
Atom Count: 3,346
Modeled Residue Count: 348
Deposited Residue Count: 546
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	C [auth D]	500	Mycobacterium phage Bxb1	Mutation(s): 0 Gene Names: 35, PBI_BXB1_35
UniProt
Find proteins for Q9B086 (Mycobacterium phage Bxb1) Explore Q9B086 Go to UniProtKB: Q9B086
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9B086
Sequence Annotations Expand
Reference Sequence

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
attB-R	A [auth G2]	22	Mycolicibacterium smegmatis
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
attB-R	B [auth H2]	24	Mycolicibacterium smegmatis
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D MOL2 format, chain D mmCIF format, chain D	D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.08 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX232F
Japan Science and Technology	Japan	JPMJCR23B6

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.