3JYU | pdb_00003jyu

Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)

• PDB DOI: https://doi.org/10.2210/pdb3JYU/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-22 Released: 2009-10-20 
• Deposition Author(s): Bacik, J.P., Avvakumov, G., Walker, J.R., Xue, S., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)

Bacik, J.P., Avvakumov, G., Walker, J.R., Xue, S., Dhe-Paganon, S.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 54.11 kDa 
• Atom Count: 3,644 
• Modeled Residue Count: 436 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase	A, B	231	Mus musculus	Mutation(s): 0  Gene Names: Usp4 EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35123 (Mus musculus) Explore P35123  Go to UniProtKB:  P35123
IMPC:  MGI:98905

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PS	C [auth B]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.06	α = 90
b = 34.06	β = 133.52
c = 125.19	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	model building
SHARP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Bacik, J.P., Avvakumov, G., Walker, J.R., Xue, S., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-10-16
  Changes: Structure summary