6O43

Crystal structure of a lysin protein from Staphylococcus phage P68


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    6PBB, 6O43

  • 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 experimental phasing ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orf11A200Staphylococcus phage P68Mutation(s): 0 
Gene Names: Orf11
UniProt
Find proteins for Q859J2 (Staphylococcus phage P68)
Explore Q859J2 
Go to UniProtKB:  Q859J2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3C (Subject of Investigation/LOI)
Query on I3C

Download Ideal Coordinates CCD File 
B [auth A]5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.397α = 90
b = 61.397β = 90
c = 101.606γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-27 
  • Released Date: 2019-07-10 
  • Deposition Author(s): Truong, J.Q.

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP150103009
Australian Research Council (ARC)AustraliaDP160101450

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence