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From the Wikipedia entry on the Protein Data Bank (PDB) (emphasis mine):

Most structures are determined by X-ray diffraction, but about 10% of structures are determined by 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.

I am currently working on an algorithm to solve distance geometry problems in the context of molecular conformations. I would prefer to test this algorithm on real data, so does the PDB contain information about the distances between pairs of atoms that were estimated from NMR spectroscopy measurements?

I checked the PDB file for the 2KB7 protein, but I only found the xyz coordinates of the atoms obtained after solving the distance geometry problem. Is it possible to get access to the estimated distances that were used to generate these conformations?

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The data can be found here:

https://bmrb.io/search/instant.php?term=2KB7

There is no link directly in the PBD as it is a one-to-many relationship. Clicking on the first value (a shifts dataset) you get somewhere in the middle a link to the actual dataset, which is a CIF like file with the following table:

                              vvvvvvv     
    1 . 1 1  2  2 MET HA H  1   4.070 . . 1 . . . A  2 MET HA . 18256 1 
    2 . 1 1  2  2 MET C  C 13 176.670 . . 1 . . . A  2 MET C  . 18256 1 
                              ^^^^^^^

Each row has the spectral shift in ppm (chevrons added) of an assigned hydrogen or carbon atom. There are also anisotropic chemical shifts and dipolar couplings datasets etc. etc. Each with a particular piece of data...

Chemical structures are "elucidated" (=solved) in different ways depending on the type of experiment.

Say you wanted only the distanced calculated by Nuclear Overhauser effect (r_NOE), you would need to find a NOE NMR experiment.

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  • $\begingroup$ Thanks a lot for your answer. I'm relatively new to the NMR literature. How are spectral/chemical shifts related to the distances between pairs of atoms in a protein? $\endgroup$
    – mhdadk
    Sep 12, 2021 at 11:07
  • $\begingroup$ Like the solutions to the phase problem in crystallography, the elucidation of the distances depends on the method used and differs between methods. However, the r_NOE mentioned above is a common technique. The elucidation of structures from a simple chemical shifts is not possible in a simple way without a myriad hacks. $\endgroup$
    – Matteo Ferla
    Sep 15, 2021 at 9:26

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