1C1M

PORCINE ELASTASE UNDER XENON PRESSURE (8 BAR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.201 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
    1C10, 1C1M, 1C3L, 1QTK

  • 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: 
    • Protein Crystallography at Ultra-Short Wavelengths: Feasability Study of Anomalous-Dispersion Experiments at the Xenon K-Edge
      Schiltz, M., Kvick, A., Svensson, O., Shepard, W., De La Fortelle, E., Prange, T., Kahn, R.
      (1997) J Synchrotron Radiat 4: 287
    • High-Pressure Krypton Gas and Statistical Heavy Atom Refinement: A Successful Combination of Tools for Macromolecular Structure Determination
      Schiltz, M., Shepard, W., Fourme, R., Prange, T., De La Fortelle, E., Bricogne, G.
      (1997) Acta Crystallogr D Biol Crystallogr 53: 78
    • The Active Site of Serine Proteinases as a Specific Binding Cavity for Xenon
      Schiltz, M., Fourme, R., Prange, T.
      (1995) Structure 3: 309
    • On the Preparation and X-Ray Data Collection of Isomorphous Xenon Derivatives
      Schiltz, M., Prange, T., Fourme, R.
      (1994) J Appl Crystallogr 27: 950

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PORCINE ELASTASE)A240Sus scrofaMutation(s): 0 
Gene Names: CELA1ELA1
EC: 3.4.21.36
Find proteins for P00772 (Sus scrofa)
Explore P00772 
Go to UniProtKB:  P00772
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XE
Query on XE

Download CCD File 
A
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.201 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.19α = 90
b = 58.22β = 90
c = 75.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Structure summary