4RXX | pdb_00004rxx

Crystal Structure of the N-terminal Domain of Human Ubiquitin Specific Protease 38

• PDB DOI: https://doi.org/10.2210/pdb4RXX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-12 Released: 2015-01-21 
• Deposition Author(s): Dong, A., Shen, L., Hu, J., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal Structure of the N-terminal Domain of Human Ubiquitin Specific Protease 38

Shen, L., Dong, A., Hu, J., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 49.66 kDa 
• Atom Count: 3,663 
• Modeled Residue Count: 426 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 38	A	430	Homo sapiens	Mutation(s): 0  Gene Names: USP38, KIAA1891 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB14 (Homo sapiens) Explore Q8NB14  Go to UniProtKB:  Q8NB14
PHAROS:  Q8NB14 GTEx:  ENSG00000170185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	UNKNOWN ATOM OR ION X

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: 2.06 Å
• R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.985	α = 90
b = 102.039	β = 90
c = 135.281	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Dong, A., Shen, L., Hu, J., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary