4RH4

Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing.

Gessmann, R.Papadovasilaki, M.Drougkas, E.Petratos, K.

(2015) Acta Crystallogr F Struct Biol Commun 71: 19-23

  • DOI: 10.1107/S2053230X14025552

  • PubMed Abstract: 
  • The copper(II) centre of the blue copper protein pseudoazurin from Alcaligenes faecalis has been substituted by zinc(II) via denaturing the protein, chelation and removal of copper and refolding the apoprotein, followed by the addition of an aqueous ...

    The copper(II) centre of the blue copper protein pseudoazurin from Alcaligenes faecalis has been substituted by zinc(II) via denaturing the protein, chelation and removal of copper and refolding the apoprotein, followed by the addition of an aqueous solution of ZnCl2. Vapour-diffusion experiments produced colourless hexagonal crystals (space group P65), which when cryocooled had unit-cell parameters a=b=49.01, c=98.08 Å. Diffraction data collected at 100 K using a copper sealed tube were phased by the weak anomalous signal of five S atoms and one Zn atom. The structure was fitted manually and refined to 1.6 Å resolution. The zinc-substituted protein exhibits similar overall geometry to the native structure with copper. Zn2+ binds more strongly to its four ligand atoms (His40 Nδ1, Cys78 Sγ, His81 Nδ1 and Met86 Sδ) and retains the tetrahedral arrangement, although the structure is less distorted than the native copper protein.


    Organizational Affiliation

    Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), N. Plastira 100, 70 013 Heraklion, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pseudoazurin
A
123Alcaligenes faecalisMutation(s): 0 
Find proteins for P04377 (Alcaligenes faecalis)
Go to UniProtKB:  P04377
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 49.005α = 90.00
b = 49.005β = 90.00
c = 98.083γ = 120.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
SHELXDphasing
SHELXEmodel building
REFMACrefinement
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references