8EFW

Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin

PDB DOI: https://doi.org/10.2210/pdb8EFW/pdb

Classification: HYDROLASE/SIGNALING PROTEIN
Organism(s): Legionella pneumophila, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-09-09 Released: 2023-09-20
Deposition Author(s): Negron Teron, K.N., Das, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Work: 0.242

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cocrystallization of ubiquitin-deubiquitinase complexes through disulfide linkage

Negron Teron, K.N., Das, C.

(2023) Acta Crystallogr D Biol Crystallogr 79: 1044-1055

DOI: https://doi.org/10.1107/S2059798323008501

Macromolecule Content

Total Structure Weight: 30.33 kDa
Atom Count: 1,851
Modelled Residue Count: 259
Deposited Residue Count: 276
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SdeA	A [auth B]	200	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for Q5ZTK4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZTK4 Go to UniProtKB: Q5ZTK4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZTK4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B [auth C]	76	Homo sapiens	Mutation(s): 1 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Work: 0.242
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.905	α = 90
b = 90.905	β = 90
c = 65.821	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-20

Deposition Author(s):

Negron Teron, K.N.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM126296-02

Revision History (Full details and data files)

Version 1.0: 2023-09-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.