1LVY

PORCINE ELASTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 53: 78-92

  • DOI: 10.1107/S0907444996009705

  • PubMed Abstract: 
  • The noble gas krypton is shown to bind to crystallized proteins in a similar way to xenon [Schiltz, Prangé & Fourme (1994). J. Appl. Cryst. 27, 950-960]. Preliminary tests show that the major krypton binding sites are essentially identical to those o ...

    The noble gas krypton is shown to bind to crystallized proteins in a similar way to xenon [Schiltz, Prangé & Fourme (1994). J. Appl. Cryst. 27, 950-960]. Preliminary tests show that the major krypton binding sites are essentially identical to those of xenon. Noticeable substitution is achieved only at substantially higher pressures (above 50 x 10(5) Pa). As is the case for xenon, the protein complexes with krypton are highly isomorphous with the native structure so that these complexes can be used for phase determination in protein crystallography. Krypton is not as heavy as xenon, but its K-absorption edge is situated at a wavelength (0.86 A) that is readily accessible on synchrotron radiation sources. As a test case, X-ray diffraction data at the high-energy side of the K edge were collected on a crystal of porcine pancreatic elastase (molecular weight of 25.9 kDa) put under a krypton gas pressure of 56 x 10(5) Pa. The occupancy of the single Kr atom is approximately 0.5, giving isomorphous and anomalous scattering strengths of 15.2 and 1.9 e, respectively. This derivative could be used successfully for phase determination with the SIRAS method (single isomorphous replacement with anomalous scattering). After phase improvement by solvent flattening, the resulting electron-density map is of exceptionally high quality, and has a correlation coefficient of 0.85 with a map calculated from the refined native structure. Careful data collection and processing, as well as the correct statistical treatment of isomorphous and anomalous signals have proven to be crucial in the determination of this electron-density map. Heavy-atom refinement and phasing were carried out with the program SHARP, which is a fully fledged implementation of the maximum-likelihood theory for heavy-atom refinement [Bricogne (1991). Crystallographic Computing 5, edited by D. Moras, A. D. Podjarny & J. C. Thierry, pp. 257-297. Oxford: Clarendon Press]. It is concluded that the use of xenon and krypton derivatives, when they can be obtained, associated with statistical heavy-atom refinement will allow one to overcome the two major limitations of the isomorphous replacement method i.e. non-isomorphism and the problem of optimal estimation of heavy-atom parameters.


    Related Citations: 
    • The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 A Resolution: Comparisons with the Structure of Alpha-Chymotrypsin
      Sawyer, L.,Shotton, D.M.,Campbell, J.W.,Wendell, P.L.,Muirhead, H.,Watson, H.C.
      (1978) J.Mol.Biol. 118: 137
    • Structure of Native Porcine Pancreatic Elastase at 1.65 A Resolutions
      Meyer, E.,Cole, G.,Radhakrishnan, R.,Epp, O.
      (1988) Acta Crystallogr.,Sect.B 44: 26
    • Amino-Acid Sequence of Porcine Pancreatic Elastase and its Homologies with Other Serine Proteinases
      Shotton, D.M.,Hartley, B.S.
      (1970) Nature 225: 802


    Organizational Affiliation

    LURE, Bâtiment 209d, Université Paris Sud, Orsay, France. schiltz@lure.u-paris.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELASTASE
A
240Sus scrofaGene Names: CELA1 (ELA1)
EC: 3.4.21.36
Find proteins for P00772 (Sus scrofa)
Go to Gene View: CELA1
Go to UniProtKB:  P00772
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.637α = 90.00
b = 57.973β = 90.00
c = 75.320γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
PROLSQrefinement
SCALAdata scaling
MOSFLMdata reduction
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance