6K6L

YGL082W-catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb6K6L/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-03 Released: 2019-07-03 
• Deposition Author(s): Lu, L.N., Wang, F.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.241 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop

Lu, L., Guo, Y., Wang, T., Liang, L., Zhao, S., Wang, F., Liu, L.

(2019) Sci China B Chem 

• DOI: https://doi.org/10.1007/s11426-019-9623-0

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 63.78 kDa 
• Atom Count: 4,486 
• Modelled Residue Count: 522 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pseudo deubiquitinase	A, B	283	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YGL082W
UniProt
Find proteins for P53155 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53155  Go to UniProtKB:  P53155

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.241 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.94	α = 90
b = 70.64	β = 102.54
c = 68.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Lu, L.N., Wang, F.

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

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description