3JYU

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.233
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P35123 (Mus musculus) Explore P35123 Go to UniProtKB: P35123
IMPC: MGI:98905
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35123
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PS Query on 1PS Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C₈ H₁₁ N O₃ S REEBJQTUIJTGAL-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.182
R-Value Observed: 0.184
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

Prepare Data

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Help and Resources

3JYU

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)