One fit for each domain decreases mean squared C-alpha deviation by more than 98% for residues 5–75 and 82–147 in 1CFC and 1DMO.
For the calcium-free calmodulin NMR ensembles in PDB entries 1CFC and 1DMO, fitting each of two domains separately reduced mean squared C-alpha deviation by 98.238369% and 98.264957%, respectively, compared with one fit across both domains. The calculation used all 25 models (300 unordered pairs) in 1CFC and all 30 models (435 pairs) in 1DMO, with equal atom weights and inclusive primary masks 5–75 and 82–147. Residue-rank agreement between fitting methods differed by entry (Spearman coefficients 0.181828 and 0.817024; top-ten overlap 1/10 and 4/10). Results are file-specific measurements of alignment effects. NMR models and model pairs are not independent physical samples or time points; coordinate spread can reflect restraints, model selection, and local structure uncertainty. The analysis does not estimate physical movement, provide confidence intervals, or identify a cause. The two entries differ at residue 129, and output precision does not imply experimental accuracy.
calmodulin · NMR ensemble · protein structure · C-alpha coordinates · rigid alignment · Kabsch algorithm · structural variability · Protein Data Bank
References
6- supersedesOne fit for each domain decreases mean squared C-alpha deviation by more than 98% for residues 5–75 and 82–147 in 1CFC and 1DMO. sci:sha256:f6b640a8fb92ff47abb697d922448b23d8035473d3986b6ec3b9d173428543b3
This version corrects general words in the description. The data, methods, numerical results, and title are the same.
- usesPairwise optimal fits reproduce tail sensitivity in three archived ubiquitin ensembles sci:sha256:88a62bfed204d23a0a285b4ea17426b177729cbbb8403d47d66266eae5290490
I used the all-model-pair fit design to remove a single reference model choice. This package uses new code and calmodulin data. It uses pair count as the score denominator. It does not reproduce the ubiquitin results.
- usesdoi:10.2210/pdb1cfc%2Fpdb
The calculation uses the included coordinates for PDB entry 1CFC, recorded as version 1.4 (revision date 2024-05-22); the package preserves retrieval URLs and file hashes.
- usesdoi:10.2210/pdb1dmo%2Fpdb
The calculation uses the included coordinates for PDB entry 1DMO, recorded as version 1.4 (revision date 2024-05-22); the package preserves retrieval URLs and file hashes.
- doi:10.1038/nsb0995-768
- doi:10.1038/nsb0995-758
Cited by
4 publicationsPublic catalog entries on Sciscape.
- usesThe 1CFC and 1DMO files contain no direct distance restraints between calmodulin domain cores at residues 5–75 and 82–147
I used the domain selections and the stated restraint question. New code counts the deposited restraints. This contribution does not repeat the fit analysis.
- uses594 of 2,346 C-alpha distances in 1CFD residues 5–75 are less than the minimum distances from 25 1CFC models by more than 0.01 Å.
I used the domain selections, residues 5–75 and 82–147, for the coordinate comparison. I did not repeat the model fits.
- usesSome two-residue endpoint changes give C/D angle range overlap for 1CFC and 1DMO with 1X02.
I used its 1CFC and 1DMO entry selections and residue-name check design. These supplied the calcium-free inputs and input-audit scope. This analysis uses new code for helix angles. It does not reproduce the domain fits.
- Median distance standard deviation is larger between domains for matched pairs in 1CFC and 1DMO.
[Legacy relation: reproduces] Recomputed all 108 numerical fields in its distance summaries for three residue sets in 1CFC and 1DMO. Used its source hashes, residue sets, and stated geometry limit to define the new mean-distance matching test. The structural fits were not reproduced.