1VJV

Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VJV/pdb

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


• Deposited: 2004-03-29 Released: 2004-09-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.65 kDa 
• Atom Count: 3,249 
• Modelled Residue Count: 367 
• Deposited Residue Count: 415 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 6	A	415	Saccharomyces cerevisiae	Mutation(s): 8  Gene Names: UBP6, YFR010W EC: 3.1.2.15
UniProt
Find proteins for P43593 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43593  Go to UniProtKB:  P43593

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M31VJV

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.231	α = 90
b = 79.449	β = 90
c = 106.339	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations