9QQ8 | pdb_00009qq8

Crystal structure of the catalytic N-terminal domain of the relaxase of plasmid pLS20 in complex with the core region

• PDB DOI: https://doi.org/10.2210/pdb9QQ8/pdb
• NAKB: 9QQ8

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


• Deposited: 2025-03-31 Released: 2026-04-15 
• Deposition Author(s): Crespo, I., Boer, D.R.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.239 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the relaxase domain of RelpLS20 in complex with sscore DNA

Crespo, I., Boer, D.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, gel filtration

Macromolecule Content 

• Total Structure Weight: 33.04 kDa 
• Atom Count: 1,711 
• Modeled Residue Count: 191 
• Deposited Residue Count: 253 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Relaxase	A	234	Bacillus subtilis subsp. natto	Mutation(s): 0
UniProt
Find proteins for E9RJ23 (Bacillus subtilis subsp. natto) Explore E9RJ23  Go to UniProtKB:  E9RJ23

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(AP*GP*TP*TP*TP*CP*CP*CP*CP*TP*TP*AP*TP*GP*CP*TP*CP*TP*T)-3')	B	19	Bacillus subtilis subsp. natto

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], D [auth A], E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.239 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.68	α = 90
b = 78.68	β = 90
c = 158.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Crespo, I., Boer, D.R.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-77883-C2-2-P
Spanish Ministry of Economy and Competitiveness	Spain	FIS2015-72574-EXP

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release
  
• Version 1.1: 2026-04-22
  Changes: Structure summary