8SSI

Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb8SSI/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia pseudomallei, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-08 Released: 2024-06-05 
• Deposition Author(s): Szczesna, M., Pruneda, J.N., Thurston, T.L.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Burkholderia esterase TssM counters RNF213-mediated bacterial ubiquitylation

Szczesna, M., Huang, Y., Lacoursiere, R.E., Bonini, F., Pol, V., Koc, F., Ward, B., Geurink, P.P., Pruneda, J.N., Thurston, T.L.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.07 kDa 
• Atom Count: 5,321 
• Modelled Residue Count: 701 
• Deposited Residue Count: 726 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deubiquitinase TssM	A, C	288	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: BPSS1512
UniProt
Find proteins for Q63K53 (Burkholderia pseudomallei (strain K96243)) Explore Q63K53  Go to UniProtKB:  Q63K53

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, D	75	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AYE	F [auth B], G [auth D]	prop-2-en-1-amine C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.517	α = 90
b = 104.517	β = 90
c = 193.801	γ = 90

Software Package:

Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Szczesna, M., Pruneda, J.N., Thurston, T.L.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM142486
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R011834/1
Wellcome Trust	United Kingdom	209411/Z/17/Z

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release