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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of yeast Otu2 OTU domain

Ikeuchi, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Ivic, N., Cheng, J., Becker, T., Ikeuchi, K.

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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  

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