6KBE | pdb_00006kbe

Structure of Deubiquitinase

PDB DOI: https://doi.org/10.2210/pdb6KBE/pdb

Classification: HYDROLASE
Organism(s): Oryza sativa Japonica Group, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-24 Released: 2020-06-24
Deposition Author(s): Lu, L.N., Liu, L., Wang, F.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.256 (Depositor), 0.259 (DCC)
R-Value Work:
0.201 (Depositor), 0.204 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6KBE

This is version 1.3 of the entry. See complete history.

Literature

Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains

Lu, L., Zhai, X., Li, X., Wang, S., Zhang, L., Wang, L., Jin, X., Liang, L., Deng, Z., Li, Z., Wang, Y., Fu, X., Hu, H., Wang, J., Mei, Z., He, Z., Wang, F.

(2022) Nat Commun 13: 4672

DOI: https://doi.org/10.1038/s41467-022-32364-3

Macromolecule Content

Total Structure Weight: 45.83 kDa
Atom Count: 3,257
Modeled Residue Count: 389
Deposited Residue Count: 405
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin thioesterase	A [auth B]	253	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: OsJ_28104 EC: 3.4.19.12
UniProt
Find proteins for B9G207 (Oryza sativa subsp. japonica) Explore B9G207 Go to UniProtKB: B9G207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9G207
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	B [auth G]	152	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
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.256 (Depositor), 0.259 (DCC)
R-Value Work: 0.201 (Depositor), 0.204 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.303	α = 90
b = 58.763	β = 90
c = 110.496	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-06-24
Type: Initial release
Version 1.1: 2022-11-09
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.