1OA1

REDUCED HYBRID CLUSTER PROTEIN (HCP) FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH STRUCTURE AT 1.55A RESOLUTION USING SYNCHROTRON RADIATION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Reduced Hybrid Cluster Proteins (Hcp) from Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at High Resolution Using Synchrotron Radiation

Aragao, D.Macedo, S.Mitchell, E.P.Romao, C.V.Liu, M.Y.Frazao, C.Saraiva, L.M.Xavier, A.V.Legall, J.Van Dongen, W.M.A.M.Hagen, W.R.Teixeira, M.Carrondo, M.A.Lindley, P.F.

(2003) J.Biol.Inorg.Chem. 8: 540

  • DOI: 10.1007/s00775-003-0443-x
  • Primary Citation of Related Structures:  1OA0
  • Also Cited By: 1W9M

  • PubMed Abstract: 
  • The hybrid cluster proteins from the sulfate reducing bacteria Desulfovibrio desulfuricans ATCC 27774 ( Dd) and Desulfovibrio vulgaris strain Hildenborough ( Dv) have been isolated and crystallized anaerobically. In each case, the protein has been re ...

    The hybrid cluster proteins from the sulfate reducing bacteria Desulfovibrio desulfuricans ATCC 27774 ( Dd) and Desulfovibrio vulgaris strain Hildenborough ( Dv) have been isolated and crystallized anaerobically. In each case, the protein has been reduced with dithionite and the crystal structure of the reduced form elucidated using X-ray synchrotron radiation techniques at 1.25 A and 1.55 A resolution for Dd and Dv, respectively. Although the overall structures of the proteins are unchanged upon reduction, there are significant changes at the hybrid cluster centres. These include significant movements in the position of the iron atom linked to the persulfide moiety in the oxidized as-isolated proteins and the sulfur atom of the persulfide itself. The nature of these changes is described and the implications with respect to the function of hybrid cluster proteins are discussed.


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, Apartado 127, 2781-901 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROXYLAMINE REDUCTASE
A
553Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)Gene Names: hcp
EC: 1.7.99.1
Find proteins for P31101 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303))
Go to UniProtKB:  P31101
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SF3
Query on SF3

Download SDF File 
Download CCD File 
A
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.053α = 90.00
b = 67.464β = 90.00
c = 134.955γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance