1OVV

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
  • Also Cited By: 2KIK

  • 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: 
    • 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
    • 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

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
A, B, C, D, E, F
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO
Download SDF File 
Download CCD File 
A, B, C, D, E, F
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B, C, D, E, F
NON-POLYMERH2 N

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.267 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.920α = 90.00
b = 80.050β = 90.00
c = 96.620γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance