6Y5T

Crystal structure of savinase at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Subtilisin SavinaseA269Lederbergia lentusMutation(s): 0 
EC: 3.4.21.62
Find proteins for P29600 (Bacillus lentus)
Explore P29600 
Go to UniProtKB:  P29600
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.704α = 90
b = 62.205β = 90
c = 75.766γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

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