1OVU

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.

Geremia, S.Di Costanzo, L.Randaccio, L.Engel, D.E.Lombardi, A.Nastri, F.DeGrado, W.F.

(2005) J Am Chem Soc 127: 17266-17276

  • DOI: 10.1021/ja054199x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu s ...

    The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands. Here, we report the di-Mn(II) and di-Co(II) derivatives of variants of this protein. Together with previously solved structures, 23 crystallographically independent four-helix bundle structures of DF1 variants have been determined, which differ in the bound metal ions and size of the active site cavity. For the di-Mn(II) derivatives, as the size of the cavity increases, the number and polarity of exogenous ligands increases. This collection of structures was analyzed to determine the relationship between protein conformation and the geometry of the active site. The primary mode of backbone movement involves a coordinated tilting and sliding of the first helix in the helix-loop-helix motif. Sliding depends on crystal-packing forces, the steric bulk of a critical residue that determines the dimensions of the active site access cavity, and the intermetal distance. Additionally, a torsional motion of the bridging carboxylates modulates the intermetal distance. This analysis provides a critical evaluation of how conformation, flexibility, and active site accessibility affect the geometry and ligand-binding properties of a metal center. The geometric parameters defining the DF structures were compared to natural diiron proteins; DF proteins have a restricted active site cavity, which may have implications for substrate recognition and chemical stability.


    Related Citations: 
    • Phasing protein structures using the group-subgroup relation.
      Di Costanzo, L., Forneris, F., Geremia, S., Randaccio, L.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1435
    • Sliding Helix Induced Change of Coordination Geomet Model Di-Mn(II) Protein
      Degrado, W.F., Di Costanzo, L., Geremia, S., Lombardi, A., Pavone, V., Randaccio, L.
      (2003) Angew Chem Int Ed Engl 42: 417
    • Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate Accessible Carboxylate-Br Dinuclear Metal Center
      Di Costanzo, L., Wade, H., Geremia, S., Randaccio, L., Pavone, V., Degrado, W.F., Lombardi, A.
      (2001) J Am Chem Soc 123: 12749
    • 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 U S A 97: 6298

    Organizational Affiliation

    Centre of Excellence in Biocrystallography, Department of Chemical Science, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy. geremia@units.it



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
four-helix bundle model di-Co(II)-DF1-L13A (form I)
A, B, C, D
50N/AMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download CCD File 
A, B, C, D
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.78α = 90
b = 147.72β = 90
c = 37.6γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Derived calculations