1AM7

Lysozyme from bacteriophage lambda


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the lysozyme from bacteriophage lambda and its relationship with V and C-type lysozymes.

Evrard, C.Fastrez, J.Declercq, J.P.

(1998) J.Mol.Biol. 276: 151-164

  • DOI: 10.1006/jmbi.1997.1499

  • PubMed Abstract: 
  • Like other lysozymes, the bacteriophage lambda lysozyme is involved in the digestion of bacterial walls. This enzyme is remarkable in that its mechanism of action is different from the classical lysozyme's mechanism. From the point of view of protein ...

    Like other lysozymes, the bacteriophage lambda lysozyme is involved in the digestion of bacterial walls. This enzyme is remarkable in that its mechanism of action is different from the classical lysozyme's mechanism. From the point of view of protein evolution, it shows features of lysozymes from different classes. The crystal structure of the enzyme in which all tryptophan residues have been replaced by aza-tryptophan has been solved by X-ray crystallography at 2.3 A using a combination of multiple isomorphous replacement, non-crystallographic symmetry averaging and density modification techniques. There are three molecules in the asymmetric unit. The characteristic structural elements of lysozymes are conserved: each molecule is organized in two domains connected by a helix and the essential catalytic residue (Glu19) is located in the depth of a cleft between the two domains. This cleft shows an open conformation in two of the independent molecules, while access to the cavity is much more restricted in the last one. A structural alignment with T4 lysozyme and hen egg white lysozyme allows us to superpose about 60 C alpha atoms with a rms distance close to 2 A. The best alignments concern the helix preceding the catalytic residue, some parts of the beta sheets and the helix joining the two domains. The results of sequence alignments with the V and C lysozymes, in which weak local similarities had been detected, are compared with the structural results.


    Related Citations: 
    • A Large Decrease in Heat-Shock-Induced Proteolysis After Tryptophan Starvation Leads to Increased Expression of Phage Lambda Lysozyme Cloned in Escherichia Coli
      Soumillion, P.,Fastrez, J.
      (1992) Biochem.J. 286: 187
    • Crystallization and Preliminary X-Ray Analysis of Bacteriophage Lambda Lysozyme in which All Tryptophans Have Been Replaced by Aza-Tryptophans
      Evrard, C.,Declercq, J.-P.,Fastrez, J.
      (1997) Acta Crystallogr.,Sect.D 53: 217
    • Is the Bacteriophage Lambda Lysozyme an Evolutionary Link or a Hybrid between the C and V-Type Lysozymes? Homology Analysis and Detection of the Catalytic Amino Acid Residues
      Jespers, L.,Sonveaux, E.,Fastrez, J.
      (1992) J.Mol.Biol. 228: 529
    • Overexpression of the Phage Lambda Lysozyme Cloned in Escherichia Coli: Use of a Degenerative Mixture of Synthetic Ribosome Binding Sites and Increase of the Protein Stability in Vivo
      Jespers, L.,Sonveaux, E.,Fastrez, J.,Phanapoulos, A.,Davison, J.
      (1991) Protein Eng. 4: 485
    • Phage Lysozymes
      Fastrez, J.
      (1996) Lysozymes: Model Enzymes in Biochemistry and Biology --: 35
    • Biosynthetic Incorporation of 7-Azatryptophan Into the Phage Lambda Lysozyme: Estimation of Tryptophan Accessibility, Effect on Enzymatic Activity and Protein Stability
      Soumillion, P.,Jespers, L.,Vervoort, J.,Fastrez, J.
      (1995) Protein Eng. 8: 451


    Organizational Affiliation

    Laboratoire de Chimie Physique et de Cristallographie, Université Catholique de Louvain, Louvain-la-Neuve Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A, B, C
158Enterobacteria phage lambdaGene Names: R
EC: 4.2.2.n2
Find proteins for P03706 (Enterobacteria phage lambda)
Go to UniProtKB:  P03706
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B, C
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRN
Query on TRN
A, B, C
L-PEPTIDE LINKINGC10 H11 N3 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.010α = 90.00
b = 78.800β = 90.00
c = 82.310γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance