Crystal structure of savinase at cryogenic conditions

Experimental Data Snapshot

  • Resolution: 0.95 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

Starting Model: experimental
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Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.

Wu, S.Nguyen, T.T.T.N.Moroz, O.V.Turkenburg, J.P.Nielsen, J.E.Wilson, K.S.Rand, K.D.Teilum, K.

(2020) PeerJ 8: e9408-e9408

  • DOI: https://doi.org/10.7717/peerj.9408
  • Primary Citation of Related Structures:  
    6Y5S, 6Y5T

  • PubMed Abstract: 

    Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown. Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals. The NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process.

  • Organizational Affiliation

    Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subtilisin Savinase269Lederbergia lentaMutation(s): 0 
Find proteins for P29600 (Lederbergia lenta)
Explore P29600 
Go to UniProtKB:  P29600
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29600
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.95 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.078α = 90
b = 62.028β = 90
c = 74.951γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark1335-00317B

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description