Answers.Body: <p>The data can be found here:</p>
  <p><a href="https://bmrb.io/search/instant.php?term=2KB7" rel="nofollow noreferrer">https://bmrb.io/search/instant.php?term=2KB7</a></p>
  <p>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:</p>
  <pre><code>                              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 
                                ^^^^^^^ 
  </code></pre>
  <p>Each row has the spectral shift in ppm (chevrons added) of an <em>assigned</em> hydrogen or carbon atom. There are also anisotropic chemical shifts and dipolar couplings datasets etc. etc. Each with a particular piece of data...</p>
  <p>Chemical structures are &quot;elucidated&quot; (=solved) in different ways depending on the type of experiment.</p>
  <p>Say you wanted only the distanced calculated by <a href="https://en.wikipedia.org/wiki/Nuclear_Overhauser_effect" rel="nofollow noreferrer">Nuclear Overhauser effect</a> (r_NOE), you would need to find a NOE NMR experiment.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-12T11:07:54.717Z
Answers.Text: 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?
Answers.UserDisplayName: mhdadk
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-15T09:26:17.197Z
Answers.Text: 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.
Answers.UserDisplayName: Matteo Ferla
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-11T08:11:09.107Z
Answers.LastActivityDate: 2021-09-11T08:11:09.107Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>From the <a href="https://en.wikipedia.org/wiki/Protein_Data_Bank" rel="nofollow noreferrer">Wikipedia entry</a> on the Protein Data Bank (PDB) (emphasis mine):</p>
  <blockquote>
  <p>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, <strong>whereas using NMR, the distance between pairs of atoms of the protein is estimated</strong>. The final conformation of the protein is obtained from NMR by solving a distance geometry problem.</p>
  </blockquote>
  <p>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?</p>
  <p>I checked the PDB file for the <a href="https://www.rcsb.org/structure/2KB7" rel="nofollow noreferrer">2KB7</a> protein, but I only found the xyz coordinates of the atoms obtained <em>after</em> solving the distance geometry problem. Is it possible to get access to the estimated distances that were used to generate these conformations?</p>
  
Tags: <protein-structure><pdb>
Title: Does the Protein Data Bank contain the estimated distances obtained using NMR spectroscopy?
ThreadText: # Does the Protein Data Bank contain the estimated distances obtained using NMR spectroscopy?
  
  (Asked by: username_0 on 2021-09-10)
  
  From the [Wikipedia entry](https://en.wikipedia.org/wiki/Protein_Data_Bank) 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](https://www.rcsb.org/structure/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?
  
  **Tags:** protein-structure, pdb
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-09-11. Score: 2 | Accepted answer
  
  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](https://en.wikipedia.org/wiki/Nuclear_Overhauser_effect) (r\_NOE), you would need to find a NOE NMR experiment.
  
  > **Comments:**
  > **username_0**: 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?  
  > **username_1**: 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.  
  
  ---
  
  