6PBB

Crystal structure of Hen Egg White Lysozyme in complex with I3C

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus

  • Deposited: 2019-06-13 Released: 2019-07-10 
  • Deposition Author(s): Truong, J.Q.
  • Funding Organization(s): Australian Research Council 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89151 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68.

Truong, J.Q.Panjikar, S.Shearwin-Whyatt, L.Bruning, J.B.Shearwin, K.E.

(2019) Acta Crystallogr D Struct Biol 75: 670-681

  • DOI: 10.1107/S2059798319009008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experim ...

    Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.


    Organizational Affiliation

    School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,MX, Australian Synchrotron, 800 Blackburn Road Clayton, Melbourne, VIC 3168, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
I3C
Query on I3C

Download SDF File 
Download CCD File 
A
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
5-Amino-2,4,6-triiodoisophthalic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89151 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.160α = 90.00
b = 77.160β = 90.00
c = 38.201γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-13 
  • Released Date: 2019-07-10 
  • Deposition Author(s): Truong, J.Q.

Funding OrganizationLocationGrant Number
Australian Research CouncilAustraliaDP150103009
Australian Research CouncilAustraliaDP160101450

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Database references