Molecular Biology Data Sources: Structure

RCSB Protein Data Bank (PDB)

What is it?

Worldwide repository for information about 3D structures of biological macromolecules e.g. ribosomes
Provides tools for structure visualization
Research Collaboratory for Structural Bioinformatics (RCSB) manages RCSB PDB
- Staff located at Rutgers University and University of California, San Diego
- A deposition, processing and distribution center for Worldwide Protein Data Bank (wwPDB)
RCSB PDB built using PDB archive, which is maintained by wwPDB
- Archive updated weekly

Access

Public access
Data files in RCSB PDB archive are free of all copyright restrictions
Molecule of the Month illustrations and articles are copyrighted
All other articles and text on the site are copyrighted
For further information on use of RCSB PDB materials, visit RCSB PDB Policies & References

How to Retrieve Data

Searching
- Where to start
  - To search for structures, enter keyword or PDB ID into search box at the top of homepage
  - Click on Author button above search box to search by author name
- Multiple search and browse options available, for more information, visit Searching the RCSB PDB
Multiple options available for download of data files, including maintaining a local copy of all PDB files
- For more information, select options from the Tool box in the right menu on the RCSB PDB homepage

Submissions

Accepts all experimentally determined structures that meet minimum requirements
- Three dimensional coordinates
- Information about composition of structure
- Information about experiment performed
- Details of structure determination steps
- Author contact information
Types of structures accepted:
- Polypeptides and their complexes
  - All gene products
  - All naturally-occurring peptides that are non-ribosomal in origin
  - All peptidic repeat units of larger polymers
  - Synthetic peptides with at least 24 residues in a polymer chain
- Polynucleotides of 4 or more residues, and their complexes
- Polysaccharides of 4 or more residues, and their complexes
RCSB PDB has several tools for the validation and deposition of data, visit RCSB PDB Data Validation & Deposition Services for more information
Length of time structure held from public release selected during deposition

What is it?

Repository of small-molecule organic and metal-organic crystal structures compiled by the Cambridge Crystallographic Data Centre (CCDC), a company that started at the University of Cambridge
Data from:
- Publications
- Private communications via direct deposit
Does not store:
- Polypeptides and polysaccharides
- Oligonucleotides
- Inorganic structures
- Metals and alloys
Part of the CSD System, which includes software for:
- Search and information retrieval
- Structure visualization
- Statistical analysis of retrieved data
- Knowledge bases derived from CSD

Access

Anyone can request data for bona fide research purposes
CSD System must be purchased
- UNC Research Computing has licenses running on Killdevil
- For further instructions on accessing CSD via Killdevil, please visit UNC Help & Support: Cambridge Structural Database

How to Retrieve Data

May request data after associated paper has been published
- Use online Request Form
- One paper per request
- Need full journal citation and CCDC Deposition Number, which should be in paper
- Data sent in CIF format free of charge
Currently only data published after 1994 is available via request
Data published before 1994 is available through CSD distributed with CSD System (see above for access instructions)

Submissions

Accepts crystal structure data from X-ray, neutron diffraction and powder studies using a constrained refinement for:
- Organic compounds
- Metal-organic compounds
- Metal carbonyls
- Boron compounds containing one or more B-H or B-OH bond and borazines
- Ring compounds containing any two of the following elements: N, P, S, Se and Te
Types of depositions:
- Pre-publication
- Published
- Private communication: structure not intended for publication
For further information, visit Deposit a Structure