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protein metals links
Electron transport PDB id
1b71
Jmol
Contents
Protein chain
191 a.a. *
Metals
_ZN
_FE ×2
Waters ×171
* Residue conservation analysis
PDB id:
1b71
Name: Electron transport
Title: Rubrerythrin
Structure: Protein (rubrerythrin). Chain: a
Source: Desulfovibrio vulgaris subsp. Vulgaris hildenborough. Organism_taxid: 882. Strain: hildenborough
Biol. unit: Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.195    
Authors: L.C.Sieker,M.Holmes,I.Le Trong,S.Turley,B.D.Santarsiero,M.-Y J.Legall,R.E.Stenkamp
Key ref:
L.C.Sieker et al. (1999). Alternative metal-binding sites in rubrerythrin. Nat Struct Biol, 6, 308-309. PubMed id: 10201393 DOI: 10.1038/7538
Date:
26-Jan-99     Release date:   26-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24931  (RUBY_DESVH) -  Rubrerythrin
Seq:
Struc: 		191 a.a.
191 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   2 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
DOI no: 10.1038/7538 Nat Struct Biol 6:308-309 (1999)
PubMed id: 10201393  
 
 
Alternative metal-binding sites in rubrerythrin.
L.C.Sieker, M.Holmes, I.Le Trong, S.Turley, B.D.Santarsiero, M.Y.Liu, J.LeGall, R.E.Stenkamp.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. a, Difference electron density (|F[o]| - |F[c]|) for aerobically purified rubrerythrin. Cyan contours are drawn at 3 . Orange contours (3 ) are shown for the Bijvoet difference density and indicate the location of atoms with significant anomalous scattering. Phases for both maps were calculated for a protein model obtained by deletion of the iron atoms and water molecules from coordinate set 1RYT, followed by five cycles of refinement to reduce model bias. Sites A, B, C and D are labeled in the figure to simplify the nomenclature and site descriptions in the text. Figure drawn with XtalView^13. b, Difference density (|F[o]| - |F[c]|) for uranyl-soaked crystals superposed on the phasing model obtained as described for (a). Cyan contours are drawn at 3 . Orange contours (3 ) and yellow contours (10 ) are shown for the Bijvoet difference density. Sites labeled as described for (a). Figure drawn with XtalView^13. c, Stereo view of the Fe−Zn complex in aerobically purified rubrerythrin. Figures drawn with MOLSCRIPT^12.
 
  The above figure is reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 308-309) copyright 1999.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
16428284 S.Sacquin-Mora, and R.Lavery (2006).
Investigating the local flexibility of functional residues in hemoproteins.
  Biophys J, 90, 2706-2717.  
15547260 M.V.Weinberg, F.E.Jenney, X.Cui, and M.W.Adams (2004).
Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase.
  J Bacteriol, 186, 7888-7895.  
12655046 D.T.Logan, E.Mulliez, K.M.Larsson, S.Bodevin, M.Atta, P.E.Garnaud, B.M.Sjoberg, and M.Fontecave (2003).
A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase.
  Proc Natl Acad Sci U S A, 100, 3826-3831.
PDB code: 1hk8
12757943 T.Wakagi (2003).
Sulerythrin, the smallest member of the rubrerythrin family, from a strictly aerobic and thermoacidophilic archaeon, Sulfolobus tokodaii strain 7.
  FEMS Microbiol Lett, 222, 33-37.  
11828492 C.M.Gomes, J.Le Gall, A.V.Xavier, and M.Teixeira (2001).
Could a diiron-containing four-helix-bundle protein have been a primitive oxygen reductase?
  Chembiochem, 2, 583-587.  
10841536 A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, and W.F.DeGrado (2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
  Proc Natl Acad Sci U S A, 97, 6298-6305.
PDB code: 1ec5
10841764 C.V.Romåo, M.Regalla, A.V.Xavier, M.Teixeira, M.Y.Liu, and J.Le Gall (2000).
A bacterioferritin from the strict anaerobe Desulfovibrio desulfuricans ATCC 27774.
  Biochemistry, 39, 6841-6849.  
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