4ZFR | pdb_00004zfr

Catalytic domain of Sst2 F403A mutant bound to ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb4ZFR/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe 972h-, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-21 Released: 2015-10-14 
• Deposition Author(s): Shrestha, R.K.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.237 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Structure of Catalytic domain of Sst2 F403A mutant bound to ubiquitin at 1.7 Angstroms

Shrestha, R.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 31.15 kDa 
• Atom Count: 2,080 
• Modeled Residue Count: 261 
• Deposited Residue Count: 278 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMSH-like protease sst2	A	197	Schizosaccharomyces pombe 972h-	Mutation(s): 1  Gene Names: sst2, SPAC19B12.10 EC: 3.4.19
UniProt
Find proteins for Q9P371 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9P371  Go to UniProtKB:  Q9P371

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	B	81	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.237 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.139	α = 90
b = 58.174	β = 109.3
c = 56.442	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Shrestha, R.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	1R01RR026273

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection, Derived calculations
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description