1BFU

SUBTILISIN CARLSBERG IN 20% DIOXANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Organic solvent binding to crystalline subtilisin1 in mostly aqueous media and in the neat solvents.

Schmitke, J.L.Stern, L.J.Klibanov, A.M.

(1998) Biochem.Biophys.Res.Commun. 248: 273-277

  • DOI: 10.1006/bbrc.1998.8937
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystal structures of the protease subtilisin Carlsberg in 40% acetonitrile and in 20% dioxane have been determined to at least 2.3 A resolution, and their solvent binding patterns have been compared to those observed in the neat organic so ...

    The X-ray crystal structures of the protease subtilisin Carlsberg in 40% acetonitrile and in 20% dioxane have been determined to at least 2.3 A resolution, and their solvent binding patterns have been compared to those observed in the neat organic solvents. The structures of the protein in the two aqueous-organic mixtures are essentially the same as in pure water, acetonitrile, and dioxane. Interestingly, the enzyme-bound organic solvent molecules tend to congregate in the active site. Three of the five bound acetonitrile molecules observed in the structure of subtilisin in 40% acetonitrile are situated in the enzyme active site, as is the single enzyme-bound dioxane molecule observed in 20% dioxane (whose location is distinct from that of any bound acetonitrile molecule). Furthermore, the organic solvent molecules detected in the enzyme active site in the aqueous-organic mixtures are in the same locations as in the structures in the corresponding neat organic solvents.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUBTILISIN CARLSBERG
A
274Bacillus licheniformisMutation(s): 0 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00780 (Bacillus licheniformis)
Go to UniProtKB:  P00780
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

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Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.555α = 90.00
b = 55.173β = 90.00
c = 53.862γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-28
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other