1JUG

LYSOZYME FROM ECHIDNA MILK (TACHYGLOSSUS ACULEATUS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the calcium-binding echidna milk lysozyme at 1.9 A resolution.

Guss, J.M.Messer, M.Costello, M.Hardy, K.Kumar, V.

(1997) Acta Crystallogr.,Sect.D 53: 355-363

  • DOI: 10.1107/S0907444996015831

  • PubMed Abstract: 
  • A lysozyme isolated from the milk of a monotreme, the echidna, Tachyglossus aculeatus multiaculeatus, has been crystallized (space group P2(1), with unit-cell dimensions a = 37.1, b = 42.0, c = 38.1 A, beta = 91 degrees and Z = 2) and the structure r ...

    A lysozyme isolated from the milk of a monotreme, the echidna, Tachyglossus aculeatus multiaculeatus, has been crystallized (space group P2(1), with unit-cell dimensions a = 37.1, b = 42.0, c = 38.1 A, beta = 91 degrees and Z = 2) and the structure refined to an R value of 0.167 for all measured data in the resolution range 7.0-1.9 A. It had previously been inferred from sequence homology with alpha-lactalbumins that echidna milk lysozyme (EML) would bind one calcium ion per molecule. This has been confirmed in the present study in which the largest peak in a difference Fourier synthesis is associated with a calcium ion. The calcium binding site of EML is very similar to that observed in baboon and human alpha-lactalbumins, and in a human lysozyme engineered to contain a calcium-binding site. The overall fold of the protein is similar to that of chick-type lysozymes. EML, like pigeon lysozyme, has only 125 residues terminating at a cysteine but in EML this forms a disulfide with a cysteine at residue 9 whereas the equivalent cysteine residue in all other lysozymes of known sequence occurs at position 6. These changes cause some minor structural rearrangements. The binding of calcium appears to have had little effect on the polypeptide backbone conformation and caused only small changes in the conformation of side chains coordinating the calcium ion. A homology modelling study [Acharya, Stuart, Phillips, McKenzie & Teahan (1994). J. Protein Chem. 13(6), 569-584] correctly predicted the overall structure of EML and the nature of its calcium binding site but generally failed to model some more subtle differences observed in the EML structure as evidenced by the fact that the homology model more closely resembles the starting structure from which the model was derived than it does the crystal structure.


    Organizational Affiliation

    Department of Biochemistry, University of Sydney, NSW, Australia. m.guss@biochem.usyd.edu.au




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
125Tachyglossus aculeatus aculeatusEC: 3.2.1.17
Find proteins for P37156 (Tachyglossus aculeatus aculeatus)
Go to UniProtKB:  P37156
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.120α = 90.00
b = 41.980β = 91.04
c = 38.090γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-10-13 
  • Released Date: 1997-04-21 
  • Deposition Author(s): Guss, J.M.

Revision History 

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance