biology

Worldwide Protein Data Bank

Worldwide Protein Data Bank is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Worldwide Protein Data Bank rather than just read about it. In short: The Worldwide Protein Data Bank (wwPDB) is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.

Worldwide Protein Data Bank — illustration

Key takeaways

Worldwide Protein Data Bank belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Worldwide Protein Data Bank to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Worldwide Protein Data Bank from memory before moving on to harder problems.

Reference excerpt

The Worldwide Protein Data Bank (wwPDB) is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The organization has five members:

Research Collaboratory for Structural Bioinformatics Protein Database (RCSB PDB) Protein Data Bank in Europe (PDBe) Protein Data Bank Japan (PDBj) Biological Magnetic Resonance Data Bank (BMRB) Electron Microscopy Data Bank (EMDB). The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB. EMDB (UK) joined in 2021. Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper". The RCSB PDB presently acts as the "archive keeper". This ensures that there is only one version of the data which is identical for all users. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public. (Data is accessed from the wwPDB website itself only through links to the member websites.) The member sites are more than just mirrors of the archive keeper, because the members offer different tools on their websites for analysing the structures in the database. Accomplishments

2008 The wwPDB now requires that, in addition to atomic coordinates, structure factor amplitudes and intensities (for crystal structure depositions) and NMR restraints (for NMR structure depositions) must be deposited as a prerequisite for receiving a PDB ID. 2007 Rolled out a remediated PDB. Remediation included changing the nomenclature to conform to IUPAC standards.

References

External links Official website Member organizations RCSB PDB, Research Collaboratory for Structural Bioinformatics Protein Databank (USA) PDBe, Protein Data Bank in Europe PDBj, Protein Data Bank Japan BMRB Archived 2020-10-20 at the Wayback Machine, Biological Magnetic Resonance Data Bank (USA) Electron Microscopy Data Bank

Worked examples

Example 1 — a first encounter with Worldwide Protein Data Bank

Start with the simplest possible case. Write down what Worldwide Protein Data Bank claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Worldwide Protein Data Bank before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Worldwide Protein Data Bank ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Worldwide Protein Data Bank

In research: Worldwide Protein Data Bank appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Worldwide Protein Data Bank in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Worldwide Protein Data Bank is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein databases, so understanding it makes those chapters shorter.
In everyday life: Look for Worldwide Protein Data Bank outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Worldwide Protein Data Bank in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Worldwide Protein Data Bank means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Worldwide Protein Data Bank out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Worldwide Protein Data Bank in simple terms?

Why does Worldwide Protein Data Bank matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Worldwide Protein Data Bank?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Worldwide Protein Data Bank.