5WJG | pdb_00005wjg

Using sound pulses to solve the crystal harvesting bottleneck

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

  • Deposited: 2017-07-22 Released: 2017-08-02 
  • Deposition Author(s): Soares, A.S., Brennan, H.M., McCarthy, L., Leroy, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Office of Workforce Development for Teachers and Scientists (WDTS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.157 (Depositor), 0.157 (DCC) 
  • R-Value Work: 
    0.124 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 
    0.125 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Using sound pulses to solve the crystal-harvesting bottleneck.

Samara, Y.N., Brennan, H.M., McCarthy, L., Bollard, M.T., Laspina, D., Wlodek, J.M., Campos, S.L., Natarajan, R., Gofron, K., McSweeney, S., Soares, A.S., Leroy, L.

(2018) Acta Crystallogr D Struct Biol 74: 986-999

  • DOI: https://doi.org/10.1107/S2059798318011506
  • Primary Citation Related Structures: 
    5WHW, 5WJG, 5WJH

  • PubMed Abstract: 

    Crystal harvesting has proven to be difficult to automate and remains the rate-limiting step for many structure-determination and high-throughput screening projects. This has resulted in crystals being prepared more rapidly than they can be harvested for X-ray data collection. Fourth-generation synchrotrons will support extraordinarily rapid rates of data acquisition, putting further pressure on the crystal-harvesting bottleneck. Here, a simple solution is reported in which crystals can be acoustically harvested from slightly modified MiTeGen In Situ-1 crystallization plates. This technique uses an acoustic pulse to eject each crystal out of its crystallization well, through a short air column and onto a micro-mesh (improving on previous work, which required separately grown crystals to be transferred before harvesting). Crystals can be individually harvested or can be serially combined with a chemical library such as a fragment library.

    • Organizational Affiliation: 
    • Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.

Macromolecule Content 

  • Total Structure Weight: 29.27 kDa 
  • Atom Count: 2,604 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 279 
  • Unique protein chains: 1

Macromolecules

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|  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: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.157 (Depositor), 0.157 (DCC) 
  • R-Value Work:  0.124 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 0.125 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.041α = 90
b = 68.041β = 90
c = 102.286γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM111244
Department of Energy (DOE, United States)United StatesKP1605010
Office of Workforce Development for Teachers and Scientists (WDTS)United States--
National Science Foundation (NSF, United States)United StatesP41GM103393

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary