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(-) Description

Title :  DESULFOFERRODOXIN FROM DESULFOVIBRIO DESULFURICANS, ATCC 27774
 
Authors :  A. V. Coelho, P. M. Matias, M. A. Carrondo
Date :  03 Sep 97  (Deposition) - 14 Oct 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Non-Heme Iron Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. V. Coelho, P. Matias, V. Fulop, A. Thompson, A. Gonzalez, M. A. Carrondo
Desulfoferrodoxin Structure Determined By Mad Phasing And Refinement To 1. 9 Angstroms Resolution Reveals A Unique Combination Of A Tetrahedral Fes4 Centre With A Square Pyramidal Fesn4 Centre
J. Biol. Inorg. Chem. V. 2 680 1997
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DESULFOFERRODOXIN
    Atcc: ATCC 27774
    Chains: A
    Collection: ATCC 27774
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FE2Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FE-1Ligand/IonFE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:9 , CYS A:12 , CYS A:28 , CYS A:29BINDING SITE FOR RESIDUE FE A 131
2AC2SOFTWAREHIS A:48 , HIS A:68 , HIS A:74 , CYS A:115 , HIS A:118BINDING SITE FOR RESIDUE FE A 132
3AC3SOFTWARESER A:87 , THR A:89 , HOH A:253BINDING SITE FOR RESIDUE CA A 150

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DFX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:63 -Gly A:64

 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DFX)

(-) Exons   (0, 0)

(no "Exon" information available for 1DFX)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:125
 aligned with DFX_DESDA | P22076 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
            DFX_DESDA     2 PKHLEVYKCTHCGNIVEVLHGGGAELVCCGEPMKHMVEGSTDGAMEKHVPVIEKVDGGYLIKVGSVPHPMEEKHWIEWIELLADGRSYTKFLKPGDAPEAFFAIDASKVTAREYCNLHGHWKAEN 126
               SCOP domains d1dfxa2 A:1-36                      d1dfxa1 A:37-125 Desulfoferrodoxin C-terminal domain                                      SCOP domains
               CATH domains 1dfxA00 A:1-125  [code=2.60.40.730, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eee...........................hhhh..eeeee..eeeee.............eeeeeeee..eeeeee.......eeeee......eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dfx A   1 PKHLEVYKCTHCGNIVEVLHGGGAELVCCGEPMKHMVEGSTDGAMEKHVPVIEKVDGGYLIKVGSVPHPMEEKHWIEWIELLADGRSYTKFLKPGDAPEAFFAIDASKVTAREYCNLHGHWKAEN 125
                                    10        20        30        40        50        60        70        80        90       100       110       120
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DFX)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (DFX_DESDA | P22076)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0050605    superoxide reductase activity    Catalysis of the reaction: superoxide + reduced rubredoxin + 2 H+ = H2O2 + rubredoxin.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

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