1OA1 | pdb_00001oa1

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

• PDB DOI: https://doi.org/10.2210/pdb1OA1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Nitratidesulfovibrio vulgaris
• Mutation(s): No 


• Deposited: 2002-12-23 Released: 2003-04-08 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.153 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

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

• PubMed: 12764602 
• DOI: https://doi.org/10.1007/s00775-003-0443-x
• Primary Citation Related Structures: 
  1OA0, 1OA1


• 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 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.

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Organizational Affiliation: 
• Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, Apartado 127, 2781-901 , Oeiras, Portugal.
European Synchrotron Radiation Facility, BP 220, 38043 Cedex, Grenoble , France.
Department of Biochemistry, University of Georgia, Athens, GA , 30602, USA.
Department of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA , Wageningen, The Netherlands.
Kluyver Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC , Delft, The Netherlands.
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, Apartado 127, 2781-901 , Oeiras, Portugal. [e-mail].
European Synchrotron Radiation Facility, BP 220, 38043 Cedex, Grenoble , France. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 60.9 kDa 
• Atom Count: 5,117 
• Modeled Residue Count: 553 
• Deposited Residue Count: 553 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYLAMINE REDUCTASE	A	553	Nitratidesulfovibrio vulgaris	Mutation(s): 0  EC: 1.7 (PDB Primary Data), 1.7.99.1 (UniProt)
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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SF3	C [auth A]	FE4-S3 CLUSTER Fe4 S3 QQACTBFBZNWJMV-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.153 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.053	α = 90
b = 67.464	β = 90
c = 134.955	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-08 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2023-03-29
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.4: 2024-05-01
  Changes: Data collection, Refinement description