8EFX

Structure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin

PDB DOI: https://doi.org/10.2210/pdb8EFX/pdb

Classification: HYDROLASE/SIGNALING PROTEIN
Organism(s): Orientia tsutsugamushi, 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: 1.85 Å
R-Value Free: 0.229
R-Value Work: 0.198
R-Value Observed: 0.200

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: 37.77 kDa
Atom Count: 2,705
Modelled Residue Count: 334
Deposited Residue Count: 335
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OtDUB	A	259	Orientia tsutsugamushi	Mutation(s): 0 Gene Names: KATO_02133
UniProt
Find proteins for A0A2U3QWA1 (Orientia tsutsugamushi) Explore A0A2U3QWA1 Go to UniProtKB: A0A2U3QWA1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2U3QWA1
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	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: 1.85 Å
R-Value Free: 0.229
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.399	α = 90
b = 83.008	β = 90
c = 99.354	γ = 90

Software Package:

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