8Y9A | pdb_00008y9a

The Crystal Structure of USP8 from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8Y9A/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-06 Released: 2024-03-06 
• Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Bao, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of USP8 from Biortus.

Wang, F., Cheng, W., Lv, Z., Ju, C., Bao, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.79 kDa 
• Atom Count: 1,089 
• Modeled Residue Count: 127 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 8	A	142	Homo sapiens	Mutation(s): 0  Gene Names: USP8, KIAA0055, UBPY EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P40818 (Homo sapiens) Explore P40818  Go to UniProtKB:  P40818
PHAROS:  P40818 GTEx:  ENSG00000138592

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.210 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.008	α = 90
b = 103.008	β = 90
c = 93.254	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Bao, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release