2W3U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.247 

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

  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • Iron Center, Substrate Recognition and Mechanism of Peptide Deformylase
      Becker, A.,Schlichting, I.,Kabsch, W.,Groche, D.,Schultz, S.,Wagner, A.F.
      (1998) Nat.Struct.Mol.Biol. 5: 1053


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE DEFORMYLASE
A
188Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: def (fms)
EC: 3.5.1.88
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6K3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.247 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.590α = 90.00
b = 54.590β = 90.00
c = 228.610γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata reduction
PHASERphasing
d*TREKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-11-30
    Type: Atomic model, Database references, Derived calculations, Refinement description
  • Version 1.3: 2014-02-19
    Type: Database references
  • Version 1.4: 2019-03-06
    Type: Data collection, Experimental preparation, Other