3UNX

Bond length analysis of asp, glu and his residues in subtilisin Carlsberg at 1.26A resolution

Summary for 3UNX

• Entry DOI: 10.2210/pdb3unx/pdb
• Related: 3UNR
• Descriptor: Subtilisin Carlsberg, GLYCEROL, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: Bacillus licheniformis
• Cellular location: Secreted: P00780
• Total number of polymer chains: 1
• Total formula weight: 27750.70

Authors

Fisher, S.J.,Helliwell, J.R.,Blakeley, M.P.,Cianci, M.,McSweeny, S. (deposition date: 2011-11-16, release date: 2012-06-27, Last modification date: 2023-09-13)

Primary citation

Fisher, S.J.,Blakeley, M.P.,Cianci, M.,McSweeney, S.,Helliwell, J.R.
Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.
Acta Crystallogr.,Sect.D, 68:800-809, 2012

PubMed Abstract: A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Å for subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65 Å for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 Å and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 Å resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 Å resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.

PubMed: 22751665
DOI: 10.1107/S0907444912012589

Experimental method

X-RAY DIFFRACTION (1.26 Å)