6PQ4

LCP-embedded Proteinase K treated with lipase

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

  • Deposited: 2019-07-08 Released: 2020-08-05 
  • Deposition Author(s): Bu, G., Zhu, L., Jing, L., Shi, D., Gonen, T., Liu, W., Nannenga, B.L.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.244 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED.

Zhu, L.Bu, G.Jing, L.Shi, D.Lee, M.Y.Gonen, T.Liu, W.Nannenga, B.L.

(2020) Structure 28: 1149-1159.e4

  • DOI: https://doi.org/10.1016/j.str.2020.07.006
  • Primary Citation of Related Structures:  
    6PQ0, 6PQ4

  • PubMed Abstract: 

    The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A 2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.


  • Organizational Affiliation

    Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.244 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.561α = 90
b = 67.561β = 90
c = 106.802γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.13-2998

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF MRI 1531991
National Science Foundation (NSF, United States)United States1231306
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR21DA042298
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM124152

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary