5WJH

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: 1.63 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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 of 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.


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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MHA (Subject of Investigation/LOI)
Query on MHA

Download Ideal Coordinates CCD File 
C [auth A](CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
C6 H10 N2 O5
QZTKDVCDBIDYMD-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.257α = 90
b = 68.257β = 90
c = 106.417γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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 StatesDMR-0936384
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)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