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PDBsum entry 3e3d
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protein ligands links
Hydrolase PDB id
3e3d

 

 

 

 

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Contents
Protein chain
129 a.a. *
Ligands
I3C ×4
EPE
Waters ×147
* Residue conservation analysis
PDB id:
3e3d
Name: Hydrolase
Title: Structure of hen egg white lysozyme with the magic triangle i3c
Structure: LysozymE C. Chain: a. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d iv. Ec: 3.2.1.17
Source: Gallus gallus. Chicken. Organism_taxid: 9031
Resolution:
1.55Å     R-factor:   0.173     R-free:   0.220
Authors: T.Beck,T.Gruene,G.M.Sheldrick
Key ref:
T.Beck et al. (2008). A magic triangle for experimental phasing of macromolecules. Acta Crystallogr D Biol Crystallogr, 64, 1179-1182. PubMed id: 19020357 DOI: 10.1107/S0907444908030266
Date:
07-Aug-08     Release date:   28-Oct-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus
Seq:
Struc: 		147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

 

 
DOI no: 10.1107/S0907444908030266 Acta Crystallogr D Biol Crystallogr 64:1179-1182 (2008)
PubMed id: 19020357  
 
 
A magic triangle for experimental phasing of macromolecules.
T.Beck, A.Krasauskas, T.Gruene, G.M.Sheldrick.
 
  ABSTRACT  
 
Obtaining phase information for the solution of macromolecular structures is still one of the bottlenecks in X-ray crystallography. 5-Amino-2,4,6-triiodoisophthalic acid (I3C), in which three covalently bound iodines form an equilateral triangle, was incorporated into proteins in order to obtain phases by single-wavelength anomalous dispersion (SAD). An improved binding capability compared with simple heavy-metal ions, ready availability, improved recognition of potential heavy-atom sites and low toxicity make I3C particularly suitable for experimental phasing.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 I3C and its interaction with proteins. (a) 5-Amino-2,4,6-triidoisophthalic acid (I3C) with three I atoms for anomalous scattering and three functional groups for hydrogen bonding. (b) One molecule of I3C in lysozyme; anomalous electron density at 4 (orange), distances in Å. The equilateral triangle formed by the I atoms is clearly visible. (c) Hydrogen bonding of the amino group of I3C with the main-chain carbonyl O atom of Asp21 in thaumatin (other interactions are not shown). (d) Interaction of I3C with three lysozyme molecules. Hydrogen bonds to Arg73 (left), Lys33 (top right) and Ser24 (bottom right) are shown by dashed lines.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 1179-1182) copyright 2008.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20382990 T.Beck, T.Gruene, and G.M.Sheldrick (2010).
The magic triangle goes MAD: experimental phasing with a bromine derivative.
  Acta Crystallogr D Biol Crystallogr, 66, 374-380.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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