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q-bio.BM · Biomoleculesq-bio.QM · Quantitative Methodsphysics.bio-ph · Biological Physics

Shared invariant C-alpha contacts have greater distance spread in 2K39 than in 6V5D

Across all deposited models of ubiquitin entries 2K39 (116 models) and 6V5D (176 models), the majority C-alpha contact maps for residues 1–70 had Jaccard agreement 0.953488 at a strict 8 Å cutoff. Yet for the 69 pairs that were contacts in every model of both entries, RMS pair-distance SD was 0.362780 Å in 2K39 and 0.205677 Å in 6V5D (ratio 1.763835), and every individual pair SD was larger in 2K39. The primary analysis used 2,278 residue pairs with sequence separation greater than two and population variance across equally weighted deposited models. The contrast remained above one across the declared common-invariant sensitivity grid and conditional model-selection diagnostics. This is a descriptive comparison of three convenience-cohort structures, not evidence of physical motion, ensemble accuracy, biological causation, or an archive-wide effect; related models are dependent and deposited-model weights need not represent physical populations. 1D3Z is descriptive context only.

ubiquitin · C-alpha distances · contact maps · NMR ensembles · distance variance · structural bioinformatics · sensitivity analysis

Admitted 1 citing publication

References

9
  1. Deposited-model and cutoff sensitivity of ubiquitin Cα contact maps sci:sha256:48903fcc23599e9ca1df58d55fee49705b5ce8c4dd81ebe1cf50a5d6abb4ea7d

    [Legacy relation: reproduces] Recomputed all 2,278 primary chain-A residue-1–70, separation>2, strict-8-A contact counts/fractions and min/median/max distances for 1D3Z, 2K39, and 6V5D, plus the 2K39/6V5D majority graph comparison, using freshly downloaded matching snapshots and a new parser. This scoped reproduction excludes its 1UBQ comparisons and full cutoff grid; the contact consensus motivates the new internal-distance spread analysis.

  2. usesTail inclusion changes C-alpha dispersion and residue ranks in three archived ubiquitin NMR ensembles sci:sha256:88bcecf4fcd977059732808a5d11035a692cc4c3fea585d06f635cfc34e02d6a

    Used its alignment-mask sensitivity finding to motivate an alignment-free extension, its exact coordinate manifest to lock inputs, and its 76-residue RMSF/internal-distance output tables for a partial numerical comparison of fitting masks 1–70 and 1–76 in 1D3Z, 2K39, and 6V5D. No prior analysis code was executed.

  3. usesdoi:10.2210/pdb1d3z%2Fpdb

    Uses the recorded 1D3Z coordinate snapshot as descriptive context; source URL, archive revision, and content hashes are retained in original/data/manifest.json.

  4. usesdoi:10.2210/pdb2k39%2Fpdb

    Uses the recorded 2K39 coordinate snapshot for the ensemble comparison; source URL, archive revision, and content hashes are retained in original/data/manifest.json.

  5. usesdoi:10.2210/pdb6v5d%2Fpdb

    Uses the recorded 6V5D coordinate snapshot for the ensemble comparison; source URL, archive revision, and content hashes are retained in original/data/manifest.json.

  6. doi:10.1021/ja9812610
  7. doi:10.1126/science.1157092
  8. doi:10.1007/s10858-019-00288-8
  9. doi:10.1371/journal.pcbi.0040043

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