3SB5

Zn-mediated Trimer of T4 Lysozyme R125C/E128C by Synthetic Symmetrization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1002/pro.727
  • Primary Citation of Related Structures:  
    3SB5, 3SB6, 3SB7, 3SB8, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysozymeA [auth B],
B [auth A],
C,
D
165Tequatrovirus T4Mutation(s): 4 
Gene Names: E
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D]
GA [auth D]
HA [auth D]
J [auth B]
K [auth B]
CA [auth D],
GA [auth D],
HA [auth D],
J [auth B],
K [auth B],
O [auth A],
R [auth A],
T [auth A],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
E [auth B]
F [auth B]
M [auth A]
AA [auth D],
BA [auth D],
E [auth B],
F [auth B],
M [auth A],
N [auth A],
V [auth C],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth D]
G [auth B]
IA [auth D]
L [auth B]
P [auth A]
EA [auth D],
G [auth B],
IA [auth D],
L [auth B],
P [auth A],
S [auth A],
X [auth C],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth D]
FA [auth D]
H [auth B]
I [auth B]
Q [auth A]
DA [auth D],
FA [auth D],
H [auth B],
I [auth B],
Q [auth A],
U [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.97α = 90
b = 128.97β = 90
c = 295.14γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations