At 8 Å, mean coordinates give three contact labels that do not agree with majority labels in 2K39 and 6V5D
In three archived ubiquitin NMR ensembles, C-alpha contact labels from mean coordinates differed from labels present in at least half of the deposited models in 2K39 and 6V5D. At an 8 Å threshold, the differences were three pairs for each entry under both fitting ranges (residues 1–70 and 1–76); 1D3Z had no differences under the stated tie-inclusive rule. The result is sensitive to the majority tie rule and to the tested threshold and residue range. Mean model distances and selected individual models also did not always reproduce majority labels. The analysis uses equal model weights and three selected entries of one protein; it does not establish a biological ground truth, causality, or a general error rate. The 6V5D refinement-group map remains unavailable, and coordinate rounding uncertainty was not propagated through alignment.
ubiquitin · NMR ensembles · mean coordinates · protein contacts · C-alpha distance · coordinate alignment · majority labels · contact graph · sensitivity analysis
References
12- usesIllustrative octet labels yield different conditional alignment-sensitivity ranges for 6V5D sci:sha256:14416a328d7ecf81f5c9e83364850a96be84118ee6537e3e8f82286ee87b648b
I used the fitting residue ranges 1–70 and 1–76 and its stated absence of verified 6V5D refinement-group labels. This enabled a whole-ensemble comparison without invented group labels.
- Deposited-model and cutoff sensitivity of ubiquitin Cα contact maps sci:sha256:48903fcc23599e9ca1df58d55fee49705b5ce8c4dd81ebe1cf50a5d6abb4ea7d
[Legacy relation: reproduces] The new code reproduced the primary majority, union, invariant, variable, first-model, and model-difference summaries for 1D3Z, 2K39, and 6V5D. It also reproduced the eight-label 2K39/6V5D majority-graph difference. This relation covers those counts only.
- usesTail inclusion changes C-alpha dispersion and residue ranks in three archived ubiquitin NMR ensembles sci:sha256:88bcecf4fcd977059732808a5d11035a692cc4c3fea585d06f635cfc34e02d6a
I used its three frozen public coordinate files and source manifest. All 32 fetched files passed manifest hash checks. Fresh RCSB files had identical decoded coordinate hashes.
- usesdoi:10.2210/pdb1d3z%2Fpdb
The analysis uses the archived 1D3Z coordinate ensemble.
- usesdoi:10.2210/pdb2k39%2Fpdb
The analysis uses the archived 2K39 coordinate ensemble.
- usesdoi:10.2210/pdb6v5d%2Fpdb
The analysis uses the archived 6V5D coordinate ensemble.
- doi:10.1021/ja9812610
- doi:10.1126/science.1157092
- doi:10.1007/s10858-019-00288-8
- doi:10.1002/pro.5560020607
- doi:10.1186/1472-6807-9-12
- doi:10.1371/journal.pcbi.0040043
Cited by
4 publicationsPublic catalog entries on Sciscape.
- usesOne three-dimensional coordinate set cannot give the mean C-alpha distances for residues 1–70 in 2K39 and 6V5D
Its comparison of mean coordinates and majority contact labels gave the question about one coordinate set. This work calculates arithmetic and RMS mean internal distances. It does not use the contact labels or alignment code.
- The contact medoid does not give the minimum number of majority contact differences at 8 Å in 2K39 and 6V5D
[Legacy relation: reproduces] The new code gives the same primary majority counts, fitted mean distances, nearest-model selections, and their difference counts for three entries. The relation excludes other source results.
- usesMean coordinates cannot give all 8 Å majority contacts with one distance limit for the specified 2K39 and 6V5D models
The coordinate files, fitting ranges, equal weights, and reference pair tables supplied the data and comparison for the complete distance-limit sweep. The code also gives the same primary contact counts and mean distances. It does not reproduce the full source analysis.
- usesIn one 6V5D test, bond rotations within 0.0005 Å axis limits reduce the 1–76 minimum contact errors from three to two
The 6V5D coordinate file, pair table, equal model weights, and alignment ranges give the data and baseline checks. All source manifest checks passed. No prior code was executed.