peptide deformylase (Ni-form) with hydrosulfide

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


A Fret Enzyme-Based Probe for Monitoring Hydrogen Sulfide.

Strianese, M.Palm, G.J.Milione, S.Kuehl, O.Hinrichs, W.Pellecchia, C.

(2012) Inorg Chem 51: 11220

  • DOI: https://doi.org/10.1021/ic301363d
  • Primary Citation of Related Structures:  
    4AL2, 4AL3, 4AZ4

  • PubMed Abstract: 

    Fluorescently labeled cobalt peptide deformylase (Co-PDF) can be efficiently used as a fluorescence-resonance-energy-transfer-based sensing device for hydrogen sulfide (H(2)S). The proof of concept of our sensor system is substantiated by spectroscopic, structural, and theoretical results. Monohydrogen sulfide coordination to Co-PDF and Ni-PDF was verified by X-ray crystallography. Density functional theory calculations were performed to gain insight into the characteristics of the coordination adduct between H(2)S and the cobalt cofactor in Co-PDF.

  • Organizational Affiliation

    Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, via Ponte Don Melillo, I-84084 Fisciano (Sa), Italy. mstriane@unisa.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
186Escherichia coli BL21(DE3)Mutation(s): 0 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.206α = 90
b = 63.222β = 144.28
c = 118.175γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Other
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 1.3: 2012-11-14
    Changes: Database references
  • Version 1.4: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description