1GN9

Hybrid Cluster Protein from Desulfovibrio desulfuricans ATCC 27774 X-ray structure at 2.6A resolution using synchrotron radiation at a wavelength of 1.722A

• PDB DOI:  https://doi.org/10.2210/pdb1GN9/pdb

• Classification: HYBRID CLUSTER
• Organism(s): Desulfovibrio desulfuricans
• Mutation(s): No 


• Deposited: 2001-10-04 Released: 2002-04-11 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

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

• PubMed: 11941509 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 118.69 kDa 
• Atom Count: 8,413 
• Modelled Residue Count: 1,086 
• Deposited Residue Count: 1,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYBRID CLUSTER PROTEIN	A, B	544	Desulfovibrio desulfuricans	Mutation(s): 0  EC: 1.7.99.1
UniProt
Find proteins for Q01770 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore Q01770  Go to UniProtKB:  Q01770

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSO	C [auth A], E [auth B]	IRON/SULFUR/OXYGEN HYBRID CLUSTER Fe4 O3 S3 NIIPGMCXXHQOSA-LVFFOBLJCB
SF4	D [auth A], F [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.4	α = 82.7
b = 61.8	β = 73.7
c = 72.2	γ = 87.3

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-11 
Deposition Author(s): 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.

Revision History  

• 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: 2019-05-08
  Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Other
• Version 3.0: 2020-12-23
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary