1QDT

2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOYSLASE SLT35 IN COMPLEX WITH CALCIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding of calcium in the EF-hand of Escherichia coli lytic transglycosylase Slt35 is important for stability.

van Asselt, E.J.Dijkstra, B.W.

(1999) FEBS Lett 458: 429-435

  • DOI: 10.1016/s0014-5793(99)01198-9
  • Primary Citation of Related Structures:  
    1QDT, 1QDR

  • PubMed Abstract: 
  • The Escherichia coli lytic transglycosylase Slt35 contains a single metal ion-binding site that resembles EF-hand calcium-binding sites. The Slt35 EF-hand is only the second observation of such a domain in a prokaryotic protein. Two crystal structures at 2 ...

    The Escherichia coli lytic transglycosylase Slt35 contains a single metal ion-binding site that resembles EF-hand calcium-binding sites. The Slt35 EF-hand is only the second observation of such a domain in a prokaryotic protein. Two crystal structures at 2.1 A resolution show that both Ca2+ ions and Na+ ions can bind to the EF-hand domain, but in subtly different configurations. Heat-induced unfolding studies demonstrate that Ca2+ ions are preferentially bound, and that only Ca2+ ions significantly increase the melting temperature of Slt35. This shows that the EF-hand calcium-binding domain is important for the stability of Slt35.


    Related Citations: 
    • Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand
      van Asselt, E.J., Dijkstra, A.J., Kalk, K.H., Takacs, B., Keck, W., Dijkstra, B.W.
      (1999) To be published --: --
    • Accelerated X-ray structure elucidation of a 36 kDa muramidase/ transglycosylase using wARP
      van Asselt, E.J., Perrakis, A., Kalk, K.H., Lamzin, V.S., Dijkstra, B.W.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 58

    Organizational Affiliation

    BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYTIC MUREIN TRANSGLYCOSYLASE BA322Escherichia coliMutation(s): 2 
EC: 4.2.2
UniProt
Find proteins for P41052 (Escherichia coli (strain K12))
Explore P41052 
Go to UniProtKB:  P41052
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.417α = 90
b = 67.788β = 90
c = 99.149γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance