2W3T

Chloro complex of the Ni-Form of E.coli deformylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the Ni(II) Complex of Escherichia Coli Peptide Deformylase and Suggestions on Deformylase Activities Depending on Different Metal(II) Centres.

Yen, N.T.H.Bogdanovic, X.Palm, G.J.Kuhl, O.Hinrichs, W.

(2010) J Biol Inorg Chem 15: 195

  • DOI: https://doi.org/10.1007/s00775-009-0583-8
  • Primary Citation of Related Structures:  
    2W3T, 2W3U

  • PubMed Abstract: 

    Crystal structures of polypeptide deformylase (PDF) of Escherichia coli with nickel(II) replacing the native iron(II) have been solved with chloride and formate as metal ligands. The chloro complex is a model for the correct protonation state of the hydrolytic hydroxo ligand and the protonated status of the Glu133 side chain as part of the hydrolytic mechanism. The ambiguity that recently some PDFs have been identified with Zn(2+) ion as the active-site centre whereas others are only active with Fe(2+) (or Co(2+), Ni(2+) is discussed with respect to Lewis acid criteria of the metal ion and substrate activation by the CD loop.


  • Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald, Greifswald, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDE DEFORMYLASE188Escherichia coli K-12Mutation(s): 0 
EC: 3.5.1.31
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Explore P0A6K3 
Go to UniProtKB:  P0A6K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6K3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.08α = 90
b = 35.98β = 113.43
c = 67.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-11-30
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description