3E3D

Structure of hen egg white lysozyme with the magic triangle I3C

• PDB DOI: https://doi.org/10.2210/pdb3E3D/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2008-08-07 Released: 2008-10-28 
• Deposition Author(s): Beck, T., Gruene, T., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

A magic triangle for experimental phasing of macromolecules

Beck, T., Krasauskas, A., Gruene, T., Sheldrick, G.M.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1179-1182

• PubMed: 19020357 
• DOI: https://doi.org/10.1107/S0907444908030266
• Primary Citation of Related Structures:  
  3E3D, 3E3S, 3E3T


• PubMed 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.

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Organizational Affiliation: 

Department of Structural Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.8 kDa 
• Atom Count: 1,219 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3C	B [auth A], C [auth A], D [auth A], E [auth A]	5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid C8 H4 I3 N O4 JEZJSNULLBSYHV-UHFFFAOYSA-N
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.220 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.83	α = 90
b = 76.83	β = 90
c = 38.87	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SADABS	data scaling
SHELXD	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Beck, T., Gruene, T., Sheldrick, G.M.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-11
  Changes: Database references
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary