1C3L

SUBTILISIN-CARLSBERG COMPLEXED WITH XENON (8 BAR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploring hydrophobic sites in proteins with xenon or krypton.

Prange, T.Schiltz, M.Pernot, L.Colloc'h, N.Longhi, S.Bourguet, W.Fourme, R.

(1998) Proteins 30: 61-73

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineat ...

    X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from Aspergillus flavus, mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis and the ligand-binding domain of the human nuclear retinoid-X receptor RXR-alpha. Under gas pressures ranging from 8 to 20 bar, xenon is able to bind to discrete sites in hydrophobic cavities, ligand and substrate binding pockets, and into the pore of channel-like structures. These xenon complexes can be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in the isomorphous replacement method of structure determination.


    Related Citations: 
    • The Structure of Subtilopeptidase 1. X-ray Crystallographic Data
      Petsko, G.A.,Tsernoglou, D.
      (1976) J.Mol.Biol. 106: 453
    • On the Preparation and X-ray Data Collection of Isomorphous Xenon Derivatives
      Schiltz, M.,Prange, T.,Fourme, R.
      (1994) J.Appl.Crystallogr. 27: 950
    • The Catalytic Site of Serine-Proteinases as a Specific Binding Cavity for Xenon
      Schiltz, M.,Fourme, R.,Broutin, I.,Prange, T.
      (1995) Structure 3: 309


    Organizational Affiliation

    LURE, Université Paris-Sud, Orsay, France. prange@lure.u-psud.fr




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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Download SDF File 
Download CCD File 
A
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.500α = 90.00
b = 55.300β = 90.00
c = 53.400γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance