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(-) Description

Title :  STRUCTURE OF FERREDOXIN
 
Authors :  T. Fujii, Y. Hata, H. Moriyama, T. Wakagi, N. Tanaka, T. Oshima
Date :  28 Aug 96  (Deposition) - 04 Sep 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Iron-Sulfur, Duplication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Fujii, Y. Hata, T. Wakagi, N. Tanaka, T. Oshima
Novel Zinc-Binding Centre In Thermoacidophilic Archaeal Ferredoxins.
Nat. Struct. Biol. V. 3 834 1996
PubMed-ID: 8836097  |  Reference-DOI: 10.1038/NSB1096-834
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERREDOXIN
    Chains: A
    Organism Scientific: SULFOLOBUS TOKODAII STR. 7
    Organism Taxid: 273063
    Strain: STRAIN 7

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1F3S2Ligand/IonFE3-S4 CLUSTER
2MLZ1Mod. Amino AcidN-METHYL-LYSINE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1F3S4Ligand/IonFE3-S4 CLUSTER
2MLZ2Mod. Amino AcidN-METHYL-LYSINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , HIS A:19 , HIS A:34 , ASP A:76BINDING SITE FOR RESIDUE ZN A 106
2AC2SOFTWARECYS A:45 , ILE A:46 , ALA A:47 , ASP A:48 , GLY A:49 , SER A:50 , CYS A:51 , TRP A:62 , CYS A:93 , ILE A:98BINDING SITE FOR RESIDUE F3S A 104
3AC3SOFTWARECYS A:55 , VAL A:57 , VAL A:59 , PHE A:60 , CYS A:83 , ILE A:84 , CYS A:86 , MET A:87 , CYS A:89BINDING SITE FOR RESIDUE F3S A 105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:23 -Pro A:24
2Pro A:27 -Pro A:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XER)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER1_SULTO36-66
75-104		  2A:35-65
A:74-103
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER1_SULTO84-95  1A:83-94
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER1_SULTO36-66
75-104		  4A:35-65
A:74-103
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER1_SULTO84-95  2A:83-94

(-) Exons   (0, 0)

(no "Exon" information available for 1XER)

(-) 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:103
 aligned with FER1_SULTO | P55907 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
           FER1_SULTO     2 GIDPNYRTNRQVVGEHSGHKVYGPVEPPKVLGIHGTIVGVDFDLCIADGSCINACPVNVFQWYDTPGHPASEKKADPVNEQACIFCMACVNVCPVAAIDVKPP 104
               SCOP domains d1xera_ A: Ferredoxin                                                                                   SCOP domains
               CATH domains 1xerA00 A:1-103  [code=3.30.70.20, no name defined]                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh..eeeee..eeee...............eee.........hhhhh......eeee........eeee...hhh.....hhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------4FE4S_FER_2  PDB: A:35-65      --------4FE4S_FER_2  PDB: A:74-103     PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------4FE4S_FER_1 --------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1xer A   1 GIDPNYRTNRQVVGEHSGHKVYGPVEPPkVLGIHGTIVGVDFDLCIADGSCINACPVNVFQWYDTPGHPASEKKADPVNEQACIFCMACVNVCPVAAIDVKPP 103
                                    10        20        30        40        50        60        70        80        90       100   
                                                       29-MLZ
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (FER1_SULTO | P55907)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.

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