2HZ8

QM/MM structure refined from NMR-structure of a single chain diiron protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: dynamical average of 300K trajectory 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

Calhoun, J.R.Liu, W.Spiegel, K.Dal Peraro, M.Klein, M.L.Valentine, K.G.Wand, A.J.Degrado, W.F.

(2008) Structure 16: 210-215

  • DOI: 10.1016/j.str.2007.11.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to ...

    We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.


    Related Citations: 
    • Computational design and characterization of a monomeric helical dinuclear metalloprotein.
      Calhoun, J.R., Kono, H., Lahr, S., Wang, W., DeGrado, W.F., Saven, J.G.
      (2003) J Mol Biol 334: 1101
    • Artificial diiron proteins: from structure to function.
      Calhoun, J.R., Nastri, F., Magloi, O., Pavone, V., Lombardi, A., DeGrado, W.F.
      (2005) Biopolymers 80: 264

    Organizational Affiliation

    Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
De novo designed diiron protein
A
115Escherichia coliMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: dynamical average of 300K trajectory 
  • OLDERADO: 2HZ8 Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance