8C3T | pdb_00008c3t

Structure of the GIsul2 transposon excisionase

• PDB DOI: https://doi.org/10.2210/pdb8C3T/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Achromobacter xylosoxidans NBRC 15126 = ATCC 27061
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-12-28 Released: 2024-01-10 
• Deposition Author(s): Smyshlyaev, G., Arinkin, V., Barabas, O.
• Funding Organization(s): European Commission, German Federal Ministry for Education and Research, EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Cryo-EM structures of transposon end complexes explain antibiotic resistance transfer across diverse bacteria

Smyshlyaev, G., Isbilir, B., Arinkin, V., Rojas-Cordova, C., Bateman, A., Barabas, O.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 8.52 kDa 
• Atom Count: 503 
• Modeled Residue Count: 57 
• Deposited Residue Count: 73 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlpA family phage regulatory protein	A	73	Achromobacter xylosoxidans NBRC 15126 = ATCC 27061	Mutation(s): 0  Gene Names: I6G72_19430
UniProt
Find proteins for A0AAN0NNU2 (Achromobacter xylosoxidans NBRC 15126 = ATCC 27061) Explore A0AAN0NNU2  Go to UniProtKB:  A0AAN0NNU2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.305	α = 90
b = 39.305	β = 90
c = 71.582	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Smyshlyaev, G., Arinkin, V., Barabas, O.

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Funding Organization	Location	Grant Number
European Commission	European Union	866250
German Federal Ministry for Education and Research	Germany	01KI1706
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND	Germany	291772

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary