Macromolecule Content

Total Structure Weight: 37.26 kDa
Atom Count: 2680
Modelled Residue Count: 317
Deposited Residue Count: 329
Unique protein chains: 2

6K9P

Structure of Deubiquitinase

PDB DOI: 10.2210/pdb6K9P/pdb

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

Deposited: 2019-06-17 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: 2.05 Å
R-Value Free: 0.210
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of Rice OTUB_like in complex with Ubiquitin at 2.047 Angstroms

Lu, L.N., Liu, L., Wang, F.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9G207
Protein Feature View 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 G]	76	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Protein Feature View Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.210
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.897	α = 90
b = 75.342	β = 92.63
c = 50.52	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

Entry History & Funding Information

Deposition Data

Deposited Date: 2019-06-17
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

RCSB PDB is 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.