7JSY | pdb_00007jsy

Proteinase K soaked with I3C determined by MicroED from a single milled microcrystal

  • Classification: HYDROLASE
  • Organism(s): Parengyodontium album
  • Mutation(s): No 

  • Deposited: 2020-08-16 Released: 2020-10-14 
  • Deposition Author(s): Martynowycz, M.W., Gonen, T.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.209 (Depositor) 
  • R-Value Work: 
    0.169 (Depositor) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7JSY

This is version 1.2 of the entry. See complete history

Literature

Ligand Incorporation into Protein Microcrystals for MicroED by On-Grid Soaking.

Martynowycz, M.W.Gonen, T.

(2021) Structure 29: 88

  • DOI: https://doi.org/10.1016/j.str.2020.09.003
  • Primary Citation Related Structures: 
    7JSY

  • PubMed Abstract: 

    A high throughout method for soaking ligands into protein microcrystals on TEM grids is presented. Every crystal on the grid is soaked simultaneously using only standard cryoelectron microscopy vitrification equipment. The method is demonstrated using proteinase K microcrystals soaked with the 5-amino-2,4,6-triodoisophthalic acid (I3C) magic triangle. A soaked microcrystal is milled to a thickness of approximately 200 nm using a focused ion beam, and MicroED data are collected. A high-resolution structure of the protein with four ligands at high occupancy is determined. Both the number of ligands bound and their occupancy is higher using on-grid soaking of microcrystals compared with much larger crystals treated similarly and investigated by X-ray crystallography. These results indicate that on-grid soaking ligands into microcrystals results in efficient uptake of ligands into protein microcrystals.


  • Organizational Affiliation
    • Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles CA90095, USA.

Macromolecule Content 

  • Total Structure Weight: 31.17 kDa 
  • Atom Count: 2,339 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 279 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.78 Å
  • R-Value Free:  0.209 (Depositor) 
  • R-Value Work:  0.169 (Depositor) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.555α = 90
b = 67.555β = 90
c = 102.773γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM136508

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary