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The missing residues in HSQC spectrum are expected to be partially solvent-exposed or have possible conformational exchange within NMR time scale.
The rest of the missing residues in the tudor protein were completed by using SWISS MODELLER [25] homology modelling server.
Notably, no information about the neighbouring subunits or the missing residues in the truncated pilin model was introduced into the fitting at any stage.
For this simulation, the missing residues in both the enzyme and carbohydrate (missing subsite −1) were generated using the CHARMM [48] program.
Gaps of missing residues in the loops of the template structure were closed by the 'Loop Search' tool implemented in Sybyl 8.1 (Tripos Inc., St .Louis, Missouri, 63144, USA).
It is unclear whether this difference indicates the start of a conformational change around the missing EF loop region or an artifact arising from incomplete constraints due to the missing residues in the model.
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In the truncated NmMpl, which lacks CD, the region corresponding to missing residues 210 215 in PaMpl is ordered even in the absence of bound metal.
A few other missing residues, located in loops, have been modeled based on homologue structures.
As described in Methods, here we model all missing residues and subunits in the T. thermophilus 70S ribosome (PDB 4V6F) [ 32] by homology modeling.
The final refined atomic model comprises residues 5 91 of monomer A and residues 10 89 for monomer B, with the missing residues not observed in the electron density (comprising the N-terminal and the C-terminal 6-his tag).
These were replaced by Mg2+, some missing residues were modeled in, and crystal waters were retained.
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