4AZ4

E.coli deformylase with Co(II) and hydrosulfide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Fret Enzyme-Based Probe for Monitoring Hydrogen Sulfide.

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

(2012) Inorg.Chem. 51: 11220

  • DOI: 10.1021/ic301363d
  • Primary Citation of Related Structures:  

  • 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 spectroscop ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE DEFORMYLASE
A
186Escherichia coli (strain B / BL21-DE3)Mutation(s): 0 
Gene Names: def
EC: 3.5.1.88
Find proteins for A0A140N556 (Escherichia coli (strain B / BL21-DE3))
Go to UniProtKB:  A0A140N556
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H2S
Query on H2S

Download SDF File 
Download CCD File 
A
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.631α = 90.00
b = 54.631β = 90.00
c = 229.416γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2012-11-14
    Type: Database references
  • Version 1.3: 2019-03-06
    Type: Data collection, Derived calculations, Experimental preparation, Other