1GNT | pdb_00001gnt

Hybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structure at 1.25A resolution using synchrotron radiation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.173 (Depositor) 
  • R-Value Work: 
    0.157 (Depositor) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1GNT

This is version 1.6 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: 514-525

  • DOI: https://doi.org/10.1007/s00775-001-0326-y
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 60.76 kDa 
  • Atom Count: 5,301 
  • Modeled Residue Count: 553 
  • Deposited Residue Count: 553 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYBRID CLUSTER PROTEIN553Nitratidesulfovibrio vulgarisMutation(s): 0 
EC: 1.7.99.1
UniProt
Find proteins for P31101 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P31101 
Go to UniProtKB:  P31101
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31101
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:  0.173 (Depositor) 
  • R-Value Work:  0.157 (Depositor) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.81α = 90
b = 64.53β = 90
c = 151.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-02-06
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.4: 2020-12-23
    Changes: Derived calculations, Other
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary