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2D-crystallization database

Data mining from a recent review by Abeyrathne et al., which tabulated successful 2D crystallization experiments from the literature, allowed us to create a database containing fields to express the physical and chemical properties of the key parameters in a 2D crystallization experiment. These include lipid composition, detergent, protein type, buffer composition (pH, salts, additives), temperature, and LPR (lipid-to-protein ratio). We also included the outcome of the experiments (crystal symmetry and unit cell dimensions), and properties of the ternary mixture between the protein (molecular weight, number of amino acids in transmembrane region, pI, etc), the lipids (alkyl chain length and saturation, headgroup, etc), and the detergent (CMC, aggregation number, etc). The database combines more than 200 crystallization conditions from about 200 papers and 150 membrane protein sequences.

Four views are available: 3 views for the properties of the ternary mixture, that is the detergent (CMC, molecular weight...), the lipids (headgroups, tail properties...) and the proteins (residues distribution, hydrophobicity...), and 1 view for the 2D crystallization screens. For the 2D crystallization screen, each entry includes the conditions leading to the successful crystallization of a given protein (pH, LPR, additives, buffer... etc). Tools allow to list the different parameters and expose some raw statistics about them.

1. Connect to www.sesame.wisc.edu/

1.a . The database can be accessed using the Jafar module at: www.sesame.wisc.edu/
1.b . Open the Jafar module:

Connect.jpg

1.c . Login: To register, simply click "new" and complete the fields.

LogIn.jpg

2. List the entries and access detailed information

Data are stored in 4 views:
  • Detergents : 1 entry per detergent or detergent mixture
  • Lipids : 1 entry per lipid. If lipids mixtures used during the crystallization, it will appear in the "screen" view
  • Proteins : 1 entry per protein; each mutant or homolog has its own entry
  • Screens : 1 entry per crystallization condition. If a protein has been successfully crystallized with 2 different lipids, 2 different entries will appear (for pH and LPR, median or optimal values are entered, unless they lead to different forms of crystals).

2.a . On the "Search" menu, select one of the 4 views you're interested in.

AccessDBviews.jpg

2.b . To see all entries, select "By owner", and leave default entries (*) to see everything.

AccessDBviews2.jpg

2.c . The list of the entries will appear in alphabetical order. Below is an example of the list for the "screen" view. The name of the entries include the acronym of the protein crystallized, the resolution obtained (diff for best diffraction spot, 2D if projection map was calculated, and 3D if 3D model was computed), a short information about the publication from which the data were extracted (name of the first author and publication year).

ProteinList.jpg

2.d . Double-click of any entry. A new window will open with detailed information concerning the 2D crystal(s):

    • Conditions used for crystal growth (ternary mixture, buffer, LPR, temperature, device...)
    • Results (oligomer, crystal types(s) and properties, link to publication and PDB/EMDB entries if available). Notes:
      • clicking on the purple button on the right hand-side of the publication field will open a webpage linking to the publication 9ncbi website).
      • when available, clicking on the purple button related to the "external references" field will open a webpage linking to the structure (emsearch.rutgers.ed for EMDB link, and www.rcsb.org for PDB files)
    • Ternary mixture properties
      .

ScreenView_AQP4.JPG

2.e . If you select a ternary mixture component and click on the purple button on the right-hand side, a new window will open with the properties of the component. Note, these views can also be access using the search button (step 2.a.), sub-menu "2d XTal Detergent", "2d XTal Lipid" or "2d XTal Protein"

3. View summaries and download data

3.a . Several reports and summaries can be accessed using the "Report" menu of the main window. Different reports are available for different views.

AccessReports.jpg

3.b . If you click on "Reports >> 2d Xtal Screen >> Details" a table including all the information from all the screens stored in the database appear:

ExportReports.jpg

3.c . The table can be saved as a cvs file if you need to extract or analyze the data with another tool: "Table Report >> Save Table File".

4. More detailed information:

Download NYSBC_2d-crystallization_database.pdf for more information.



-- NicolasCoudray - 19 Sep 2013

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