Editing Protein Data Bank (section)

==Contents==
The PDB database is updated weekly ([[Coordinated Universal Time|UTC]]+0 Wednesday), along with its holdings list.<ref>{{cite web |url=http://www.rcsb.org/pdb/statistics/holdings.do |title=PDB Current Holdings Breakdown |publisher=RCSB |access-date=2007-07-02 |archive-date=2007-07-04 |archive-url=https://web.archive.org/web/20070704045207/http://www.rcsb.org/pdb/statistics/holdings.do |url-status=dead }}</ref> {{As of|2023|01|10}}, the PDB comprised:
{| border="0" style="border: 1px solid #999; background-color:#FFFFFF"
|-align="center" bgcolor="#CCCCCC"
!Experimental<br/>Method
![[Protein]]s only
!Proteins with oligosaccharides
!Protein/Nucleic Acid<br/>complexes
![[Nucleic acid|Nucleic Acids]] only
!Other
!Oligosaccharides only
!Total
|-align="right"
|align="left"|[[X-ray crystallography|X-ray diffraction]] || 152277 || 8969 || 8027 || 2566 || 163 ||11 || 172013
|--bgcolor="#EFEFEF" align="right"
|align="left"|[[Nuclear magnetic resonance spectroscopy of proteins|NMR]] || 12104 || 32 || 281 || 1433 || 31 || 6 || 13887
|-align="right"
|align="left"|[[Cryo-electron microscopy|Electron microscopy]] || 9226 || 1633 || 2898 || 77 || 8 || 0 || 13842
|--bgcolor="#EFEFEF" align="right"
|align="left"|Hybrid || 189 || 7 || 6 || 12 || 0 || 1 || 215
|-align="right"
|align="left"|Neutron || 72 || 1 || 0 || 2 || 0 || 0 || 75
|-align="right"
|align="left"|Other || 32 || 0 || 0 || 1 || 0 || 4 || 309
|--bgcolor="#EFEFEF" align="right"
|''Total:'' || 173900 || 10642 || 11212 || 4091 ||  202 || 22 || 200069
|}
::162,041 structures in the PDB have a [[structure factor]] file.
::11,242 structures have an NMR restraint file.
::5,774 structures in the PDB have a [[chemical shift]]s file.
::13,388 structures in the PDB have a [[3DEM]] map file deposited in [[EM Data Bank]]

[[File:Rate of Protein Structure Determination-2019b.png|thumb|upright=1.5|Rate of protein structure determination techniques over the decades. MX = macromolecular [[crystallography]], 3DEM = 3D [[Electron microscope|Electron microscopy]].<ref>{{cite journal | vauthors = Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Costanzo LD, etal | collaboration = wwPDB consortium | title = Protein Data Bank: the single global archive for 3D macromolecular structure data | journal = Nucleic Acids Research | volume = 47 | issue = D1 | pages = D520–D528 | date = January 2019 | pmid = 30357364 | pmc = 6324056 | doi = 10.1093/nar/gky949 }}</ref>]]

Most structures are determined by X-ray diffraction, but about 7% of structures are determined by [[nuclear magnetic resonance spectroscopy of proteins|protein NMR]]. When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas using NMR, the distance between pairs of atoms of the protein is estimated. The final conformation of the protein is obtained from NMR by solving a [[distance geometry]] problem. After 2013, a growing number of proteins are determined by [[cryo-electron microscopy]]. 

For PDB structures determined by X-ray diffraction that have a structure factor file, their electron density map may be viewed. The data of such structures may be viewed on the three PDB websites. 

Historically, the number of structures in the PDB has grown at an approximately exponential rate, with 100 registered structures in 1982, 1,000 structures in 1993, 10,000 in 1999, 100,000 in 2014, and 200,000 in January 2023.<ref>{{Cite journal| author = Anon | doi = 10.1038/509260a| pmid = 24834514| title = Hard data: It has been no small feat for the Protein Data Bank to stay relevant for 100,000 structures| journal = Nature| volume = 509| issue = 7500| pages = 260| year = 2014| doi-access = free}}</ref><ref>{{cite web |last1=Protein Data Bank |title=PDB Statistics: Overall Growth of Released Structures Per Year |url=https://www.rcsb.org/stats/growth/growth-released-structures |website=www.rcsb.org |access-date=12 January 2023}}</ref>