3SB8

Cu-mediated Dimer of T4 Lysozyme D61H/K65H by Synthetic Symmetrization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An approach to crystallizing proteins by metal-mediated synthetic symmetrization.

Laganowsky, A.Zhao, M.Soriaga, A.B.Sawaya, M.R.Cascio, D.Yeates, T.O.

(2011) Protein Sci. 20: 1876-1890

  • DOI: 10.1002/pro.727
  • Primary Citation of Related Structures:  3SB5, 3SB6, 3SB7, 3SB9, 3SBA, 3SBB, 3SER, 3SES, 3SET, 3SEU, 3SEV, 3SEW, 3SEX, 3SEY

  • PubMed Abstract: 
  • Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cystein ...

    Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu²⁺, nickel (Ni²⁺), or zinc (Zn²⁺). The approach resulted in 16 new crystal structures--eight for T4L and eight for MBP--displaying a variety of oligomeric assemblies and packing modes, representing in total 13 new and distinct crystal forms for these proteins. We discuss the potential utility of the method for crystallizing target proteins of unknown structure by engineering in pairs of histidine or cysteine residues. As an alternate strategy, we propose that the varied crystallization-prone forms of T4L or MBP engineered in this work could be used as crystallization chaperones, by fusing them genetically to target proteins of interest.


    Organizational Affiliation

    Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095-1570, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B, C
165Enterobacteria phage T4Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.880α = 90.00
b = 95.180β = 90.00
c = 117.020γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-11-02
    Type: Database references