1QDR | pdb_00001qdr

2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35

• PDB DOI: https://doi.org/10.2210/pdb1QDR/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-07-10 Released: 2000-01-24 
• Deposition Author(s): van Asselt, E.J., Dijkstra, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

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

• PubMed: 10570954 
• DOI: https://doi.org/10.1016/s0014-5793(99)01198-9
• Primary Citation of Related Structures:  
  1QDR, 1QDT


• 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 2.1 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.33 kDa 
• Atom Count: 2,863 
• Modelled Residue Count: 312 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYTIC MUREIN TRANSGLYCOSYLASE B	A	322	Escherichia coli	Mutation(s): 2  EC: 3.2.1
UniProt
Find proteins for P41052 (Escherichia coli (strain K12)) Explore P41052  Go to UniProtKB:  P41052

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCN	C [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.533	α = 90
b = 67.799	β = 90
c = 98.72	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-24 
Deposition Author(s): van Asselt, E.J., Dijkstra, A.J.

Revision History  

• 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: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection