1EC5

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.

Lombardi, A.Summa, C.M.Geremia, S.Randaccio, L.Pavone, V.DeGrado, W.F.

(2000) Proc.Natl.Acad.Sci.USA 97: 6298-6305

  • Also Cited By: 1U7J, 1U7M

  • PubMed Abstract: 
  • De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins. The metal-binding sites of many metalloproteins lie between multiple elements of secondary s ...

    De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins. The metal-binding sites of many metalloproteins lie between multiple elements of secondary structure, inviting a retrostructural approach to constructing minimal models of their active sites. The backbone geometries comprising the metal-binding sites of zinc fingers, diiron proteins, and rubredoxins may be described to within approximately 1 A rms deviation by using a simple geometric model with only six adjustable parameters. These geometric models provide excellent starting points for the design of metalloproteins, as illustrated in the construction of Due Ferro 1 (DF1), a minimal model for the Glu-Xxx-Xxx-His class of dinuclear metalloproteins. This protein was synthesized and structurally characterized as the di-Zn(II) complex by x-ray crystallography, by using data that extend to 2.5 A. This four-helix bundle protein is comprised of two noncovalently associated helix-loop-helix motifs. The dinuclear center is formed by two bridging Glu and two chelating Glu side chains, as well as two monodentate His ligands. The primary ligands are mostly buried in the protein interior, and their geometries are stabilized by a network of hydrogen bonds to second-shell ligands. In particular, a Tyr residue forms a hydrogen bond to a chelating Glu ligand, similar to a motif found in the diiron-containing R2 subunit of Escherichia coli ribonucleotide reductase and the ferritins. DF1 also binds cobalt and iron ions and should provide an attractive model for a variety of diiron proteins that use oxygen for processes including iron storage, radical formation, and hydrocarbon oxidation.


    Related Citations: 
    • Tertiary Templates for the Design of Diiron Protein
      Summa, C.M.,Lombardi, A.,Lewis, M.,Degrado, W.F.
      (1999) Curr.Opin.Struct.Biol. 9: 500
    • De Novo Design and Structural Characterization of Proteins and Metalloproteins
      Degrado, W.F.,Summa, C.M.,Pavone, V.,Nastri, F.,Lombardi, A.
      (1999) Annu.Rev.Biochem. 68: 779


    Organizational Affiliation

    Department of Chemistry, University of Napoli "Federico II," Via Mezzocannone, 4, I-80134 Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FOUR-HELIX BUNDLE MODEL)
A, B, C
50N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B, C
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B, C
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 36.070α = 90.00
b = 89.160β = 90.00
c = 79.890γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-01-25 
  • Released Date: 2000-07-26 
  • Deposition Author(s): Geremia, S.

Revision History 

  • Version 1.0: 2000-07-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation