PDBsum entry 1lvy

Serine protease

PDB id: 1lvy

Contents

Protein chain

240 a.a. *

Ligands

SO4

Metals

_CA

Waters ×79

* Residue conservation analysis

PDB id:

1lvy

Name:

Serine protease

Title:

Porcine elastase

Structure:

Elastase. Chain: a. Ec: 3.4.21.36

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas

Resolution:

1.87Å R-factor: 0.185 R-free: 0.229

Authors:

M.Schiltz,T.Prange

Key ref:

M.Schiltz et al. (1997). High-pressure krypton gas and statistical heavy-atom refinement: a successful combination of tools for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr, 53, 78-92. PubMed id: 15299973 DOI: 10.1107/S0907444996009705

Date:

20-Jul-96 Release date: 27-Jan-97

Protein chain

P00772  (CELA1_PIG) -  Chymotrypsin-like elastase family member 1 from Sus scrofa

Seq: 266 a.a.

Struc: 240 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.21.36 - pancreatic elastase.
• Reaction: Hydrolysis of proteins, including elastin. Preferential cleavage: Ala-|-Xaa.

DOI no: 10.1107/S0907444996009705

Acta Crystallogr D Biol Crystallogr 53:78-92 (1997)

PubMed id: 15299973

High-pressure krypton gas and statistical heavy-atom refinement: a successful combination of tools for macromolecular structure determination.

M.Schiltz, W.Shepard, R.Fourme, T.Prangé, E.de la Fortelle, G.Bricogne.

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 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.

Selected figure(s)

Figure 3.
Fig. 3. Isotherrns (293 K) of xenon and krypton binding to PPE. The quantity p/k, which is equivalent to the occupancy of the heavy atom, is plotted versus the gas pressure P. p is the nlaximum density (corresponding to the bound heavy atom) in a difference-Fourier ,nap and k is a normalization factor that was obtained for each curve by least-squares fitting of the experimental data points (p,P) to the function, p/k = AP/(I + AP) The lined curves are shown as dashed lines.

Figure 4.
Fig. 4. Fluorescence spectrum of krypton gas.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1997, 53, 78-92) copyright 1997.

Figures were selected by an automated process.