7PL7 | pdb_00007pl7

Crystal structure of yeast Otu2 OTU domain

PDB DOI: https://doi.org/10.2210/pdb7PL7/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-08-28 Released: 2022-09-07
Deposition Author(s): Ivic, N., Cheng, J., Becker, T., Ikeuchi, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.264 (Depositor), 0.276 (DCC)
R-Value Work:
0.225 (Depositor), 0.235 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of yeast Otu2 OTU domain

Ikeuchi, K.

To be published.

Macromolecule Content

Total Structure Weight: 19.45 kDa
Atom Count: 1,322
Modeled Residue Count: 155
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OTU domain-containing protein 2	A	165	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: OTU2, YHL013C
UniProt
Find proteins for P38747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38747 Go to UniProtKB: P38747
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38747
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264 (Depositor), 0.276 (DCC)
R-Value Work: 0.225 (Depositor), 0.235 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.669	α = 90
b = 60.055	β = 90
c = 148.349	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-07

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB/TRR-174
German Research Foundation (DFG)	Germany	BE1814/15-1
German Research Foundation (DFG)	Germany	BE1814/1-1

Revision History (Full details and data files)

Version 1.0: 2022-09-07
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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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.