Difference between revisions of "BIN-PDB"

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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
The RCSB-PDB Structure Database
 
The RCSB-PDB Structure Database
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(The RCSB PDB database and services)
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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The RCSB PDB database and services
 
 
</div>
 
</div>
  
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{{Smallvspace}}
  
  
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__TOC__
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "abstract" -->
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This unit provides a short introduction to the PDB.
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...
 
 
<section end=abstract />
 
<section end=abstract />
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</div>
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<!-- ============================  -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
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This unit will ...
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You need to complete the following units before beginning this one:
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* ... introduce the PDB and explore its use.
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* ... can navigate and use the PDB.
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</td>
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</tr>
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</table>
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<!-- ============================ -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
 +
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
 +
This unit builds on material covered in the following prerequisite units:<br />
 
*[[BIN-Databases|BIN-Databases (Bioinformatics Databases)]]
 
*[[BIN-Databases|BIN-Databases (Bioinformatics Databases)]]
 
*[[BIN-SX-Concepts|BIN-SX-Concepts (Concepts of Molecular Structure)]]
 
*[[BIN-SX-Concepts|BIN-SX-Concepts (Concepts of Molecular Structure)]]
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<section end=prerequisites />
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<!-- ============================  -->
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</div>
  
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=== Objectives ===
 
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "objectives" -->
 
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...
 
  
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=== Outcomes ===
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__TOC__
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "outcomes" -->
 
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...
 
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=== Deliverables ===
 
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "evaluation" -->
 
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<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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== Contents ==
 
== Contents ==
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "contents" -->
 
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{{Task|1=
 
{{Task|1=
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* Read
 
* Read
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{{#pmid: 27794042}}
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{{#pmid: 30357411}}
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{{#pmid: 27603019}}
 
  
 
}}
 
}}
  
  
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==The PDB==
 
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; Search for GO and EC numbers at PDB...
 
  
 
The search options in the PDB structure database are as sophisticated as those at the NCBI. For now, we will try a simple keyword search to get us started.
 
The search options in the PDB structure database are as sophisticated as those at the NCBI. For now, we will try a simple keyword search to get us started.
  
  
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{{task|
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{{task|1=
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# Visit the RCSB PDB website at http://www.pdb.org/
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* Visit the RCSB PDB website at http://www.rcsb.org/pdb
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# Briefly orient yourself regarding the database contents and its information offerings and services.
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* Briefly orient yourself regarding the database contents and its information offerings and services.
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# Enter <code>Mbp1</code> into the search field.
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* Enter <code>Mbp1</code> into the search field.
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# In your journal, note down the PDB IDs for the three ''Saccharomyces cerevisiae'' Mbp1 transcription factor structures your search has retrieved.
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* In your journal, note down the PDB IDs for the three ''Saccharomyces cerevisiae'' Mbp1 transcription factor structures your search has retrieved.
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# Click on one of the entries and explore the information and services linked from that page.
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* Click on [http://www.rcsb.org/pdb/explore/explore.do?structureId=1BM8 1BM8] entry and explore the information and services linked from that page.
 +
**On the '''Structure Summary''' tab, note that this structure has 1.71&Aring; resolution - which is very high. The protein feature view shows where the domain is located in the full-length protein. This page has a download link, from which you can get the PDB coordinates file, as well as the biological assembly (whenver that is relevant).
 +
**On the '''3D View''' tab, explore the visualization options. The default view is the Mol* molecular viewer. Have a look at the [https://www.rcsb.org/3d-view/molstar/help/getting-started Help page] and explore the options. Can you ...
 +
***...change the color of the molecule?
 +
***...display a molecular surface?
 +
***...change the representation to ball-and-stick?
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** On the '''Annotations''' tab, explore the cross-references. Pursue the link to the "Mlu1-box Binding Protein; DNA-binding Domain" annotation of the CATH database domain annotations at the Topology level, to see how many proteins with a similar fold are held in the PDB.
 +
** Explore the other tabs, and take special note of the '''Structure Similarity''' tab. This is one of the important resources, the ability to find and superimpose similar structures helps tremendously in interpreting e.g. conservation patterns in a protein.
 
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* [http://www.wwpdb.org/documentation/format23/v2.3.html '''PDB file format''']
 
* [http://www.wwpdb.org/documentation/format23/v2.3.html '''PDB file format''']
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== Notes ==
 
== Notes ==
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<!-- included from "../components/BIN-PDB.components.wtxt", section: "notes" -->
 
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== Self-evaluation ==
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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<div class="about">
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-09-22
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.1 Maintenance
 +
*1.0.1 Removed inaccessible article by Costanzo ''et.al'' and updated NAR article
 +
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 09:26, 25 September 2020

The RCSB-PDB Structure Database

(The RCSB PDB database and services)


 


Abstract:

This unit provides a short introduction to the PDB.

Objectives:
This unit will ...

  • ... introduce the PDB and explore its use.

Outcomes:
After working through this unit you ...

  • ... can navigate and use the PDB.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

    • Prerequisites:
    This unit builds on material covered in the following prerequisite units:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:

    • Read
    Burley et al. (2019) RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res 47:D464-D474. (pmid: 30357411)

    [ PubMed ] [ DOI ] The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'


    The search options in the PDB structure database are as sophisticated as those at the NCBI. For now, we will try a simple keyword search to get us started.


    Task:

    • Visit the RCSB PDB website at http://www.rcsb.org/pdb
    • Briefly orient yourself regarding the database contents and its information offerings and services.
    • Enter Mbp1 into the search field.
    • In your journal, note down the PDB IDs for the three Saccharomyces cerevisiae Mbp1 transcription factor structures your search has retrieved.
    • Click on 1BM8 entry and explore the information and services linked from that page.
      • On the Structure Summary tab, note that this structure has 1.71Å resolution - which is very high. The protein feature view shows where the domain is located in the full-length protein. This page has a download link, from which you can get the PDB coordinates file, as well as the biological assembly (whenver that is relevant).
      • On the 3D View tab, explore the visualization options. The default view is the Mol* molecular viewer. Have a look at the Help page and explore the options. Can you ...
        • ...change the color of the molecule?
        • ...display a molecular surface?
        • ...change the representation to ball-and-stick?
      • On the Annotations tab, explore the cross-references. Pursue the link to the "Mlu1-box Binding Protein; DNA-binding Domain" annotation of the CATH database domain annotations at the Topology level, to see how many proteins with a similar fold are held in the PDB.
      • Explore the other tabs, and take special note of the Structure Similarity tab. This is one of the important resources, the ability to find and superimpose similar structures helps tremendously in interpreting e.g. conservation patterns in a protein.


    Further reading, links and resources

    Notes


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-22

    Version:

    1.1

    Version history:

    • 1.1 Maintenance
    • 1.0.1 Removed inaccessible article by Costanzo et.al and updated NAR article
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-PDB&oldid=11686"