3D43

The crystal structure of Sph at 0.8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state.

Almog, O.Gonzalez, A.Godin, N.de Leeuw, M.Mekel, M.J.Klein, D.Braun, S.Shoham, G.Walter, R.L.

(2009) Proteins 74: 489-496

  • DOI: 10.1002/prot.22175
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We determine and compare the crystal structure of two proteases belonging to the subtilisin superfamily: S41, a cold-adapted serine protease produced by Antarctic bacilli, at 1.4 A resolution and Sph, a mesophilic serine protease produced by Bacillus ...

    We determine and compare the crystal structure of two proteases belonging to the subtilisin superfamily: S41, a cold-adapted serine protease produced by Antarctic bacilli, at 1.4 A resolution and Sph, a mesophilic serine protease produced by Bacillus sphaericus, at 0.8 A resolution. The purpose of this comparison was to find out whether multiple calcium ion binding is a molecular factor responsible for the adaptation of S41 to extreme low temperatures. We find that these two subtilisins have the same subtilisin fold with a root mean square between the two structures of 0.54 A. The final models for S41 and Sph include a calcium-loaded state of five ions bound to each of these two subtilisin molecules. None of these calcium-binding sites correlate with the high affinity known binding site (site A) found for other subtilisins. Structural analysis of the five calcium-binding sites found in these two crystal structures indicate that three of the binding sites have two side chains of an acidic residue coordinating the calcium ion, whereas the other two binding sites have either a main-chain carbonyl, or only one acidic residue side chain coordinating the calcium ion. Thus, we conclude that three of the sites are of high affinity toward calcium ions, whereas the other two are of low affinity. Because Sph is a mesophilic subtilisin and S41 is a psychrophilic subtilisin, but both crystal structures were found to bind five calcium ions, we suggest that multiple calcium ion binding is not responsible for the adaptation of S41 to low temperatures.


    Organizational Affiliation

    Department of Clinical Biochemistry, Faculty of Health Sciences, Ben-Gurion University, Beer Sheva 84105, Israel. almogo@bgu.ac.il




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sphericase
A, B
310Lysinibacillus sphaericusMutation(s): 0 
Find proteins for Q9S3L6 (Lysinibacillus sphaericus)
Go to UniProtKB:  Q9S3L6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.088α = 90.00
b = 62.668β = 95.47
c = 84.874γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALAdata scaling
SHELXmodel building
MOLREPphasing
MAR345dtbdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-05-13 
  • Released Date: 2009-04-28 
  • Deposition Author(s): Almog, O.

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description, Source and taxonomy