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 2.1 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: 10.1007/s00775-001-0326-y
  • Primary Citation of Related Structures:  
    1GNL, 1GNT, 1GN9

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYBRID CLUSTER PROTEINA, B544Desulfovibrio desulfuricansMutation(s): 0 
EC: 1.7.99.1
Find proteins for Q01770 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore Q01770 
Go to UniProtKB:  Q01770
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSO
Query on FSO

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]IRON/SULFUR/OXYGEN HYBRID CLUSTER
Fe4 O3 S3
NIIPGMCXXHQOSA-LVFFOBLJCB
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
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

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Entry History 

Deposition Data

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