1GNL

Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Hybrid Cluster Proteins (Hcps) from Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at 1.25 A Resolution Using Synchrotron Radiation.

Macedo, S.Mitchell, E.P.Romao, C.V.Cooper, S.J.Coelho, R.Liu, M.Y.Xavier, A.V.Legall, J.Bailey, S.Garner, D.C.Hagen, W.R.Teixeira, M.Carrondo, M.A.Lindley, P.

(2002) J Biol Inorg Chem 7: 514

  • DOI: https://doi.org/10.1007/s00775-001-0326-y
  • Primary Citation of Related Structures:  
    1GN9, 1GNL, 1GNT

  • PubMed Abstract: 

    The structures of the hybrid cluster proteins (HCPs) from the sulfate-reducing bacteria Desulfovibrio desulfuricans (ATCC 27774) and Desulfovibrio vulgaris (Hildenborough) have been elucidated at a resolution of 1.25 A using X-ray synchrotron radiation techniques. In the case of the D. desulfuricans protein, protein isolation, purification, crystallization and X-ray data collection were carried out under strict anaerobic conditions, whereas for the D. vulgaris protein the conditions were aerobic. However, both structures are essentially the same, comprising three domains and two iron-sulfur centres. One of these centres situated near the exterior of the molecules in domain 1 is a cubane [4Fe-4S] cluster, whereas the other, located at the interface of the three domains, contains the unusual four-iron cluster initially found in the D. vulgaris protein. Details of the structures and the associated EPR spectroscopy of the D. desulfuricans protein are reported herein. These structures show that the nature of the hybrid cluster, containing both oxygen and sulfur bridges, is independent of the presence of oxygen in the isolation and crystallization procedure and also does not vary significantly with changes in the oxidation state. The structures and amino acid sequences of the HCP are compared with the recently elucidated structure of the catalytic subunit of a carbon monoxide dehydrogenase from Carboxydothermus hydrogenoformans and related dehydrogenases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0326-y.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYBRID CLUSTER PROTEIN
A, B
544Desulfovibrio desulfuricansMutation(s): 0 
UniProt
Find proteins for Q01770 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore Q01770 
Go to UniProtKB:  Q01770
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01770
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.33α = 82.77
b = 61.65β = 73.67
c = 72.25γ = 87.31
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-11
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 2.0: 2019-03-06
    Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.1: 2020-12-23
    Changes: Derived calculations
  • Version 2.2: 2023-12-13
    Changes: Data collection, Database references, Refinement description