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(-) Description

Title :  THE CRYSTAL STRUCTURE OF FDXA, A 7FE FERREDOXIN FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  S. Ricagno, M. De Rosa, A. Aliverti, G. Zanetti, M. Bolognesi
Date :  06 Jun 07  (Deposition) - 03 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Iron, Transport, Iron-Sulfur, Mycobacterium Tuberculosis, Fe-S Cluster, Metal-Binding, 7Fe Ferredoxin, Electron Transfer, Electron Transport, Mycobacterium Smegmatis, 4Fe-4S Cluster Instability (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ricagno, M. De Rosa, A. Aliverti, G. Zanetti, M. Bolognesi
The Crystal Structure Of Fdxa, A 7Fe Ferredoxin From Mycobacterium Smegmatis.
Biochem. Biophys. Res. Commun. V. 360 97 2007
PubMed-ID: 17577575  |  Reference-DOI: 10.1016/J.BBRC.2007.06.013

(-) Compounds

Molecule 1 - FERREDOXIN
    ChainsA, B
    FragmentRESIDUES 1-105
    Organism ScientificMYCOBACTERIUM SMEGMATIS
    Organism Taxid246196
    StrainMC2
    Synonym7-IRON FERREDOXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CSS2Mod. Amino AcidS-MERCAPTOCYSTEINE
3F3S4Ligand/IonFE3-S4 CLUSTER
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
3F3S2Ligand/IonFE3-S4 CLUSTER
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
3F3S2Ligand/IonFE3-S4 CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:2 , CYS A:20 , CYS A:24 , CYS A:39 , VAL A:40 , CSS A:42 , GLY A:43 , ALA A:44 , CYS A:45BINDING SITE FOR RESIDUE F3S A 107
2AC2SOFTWAREILE A:4 , CYS A:8 , LYS A:12 , ASP A:13 , LYS A:14 , ALA A:15 , CYS A:16 , CYS A:49BINDING SITE FOR RESIDUE F3S A 108
3AC3SOFTWARETYR B:2 , CYS B:20 , CYS B:24 , CYS B:39 , VAL B:40 , CSS B:42 , GLY B:43 , ALA B:44 , CYS B:45BINDING SITE FOR RESIDUE F3S B 107
4AC4SOFTWARECYS B:8 , LYS B:12 , ASP B:13 , LYS B:14 , ALA B:15 , CYS B:16 , LEU B:32 , CYS B:49BINDING SITE FOR RESIDUE F3S B 108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V2K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V2K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V2K)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_MYCSM30-59
 
  2A:30-59
B:30-59
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER_MYCSM39-50
 
  2A:39-50
B:39-50
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_MYCSM30-59
 
  1A:30-59
-
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER_MYCSM39-50
 
  1A:39-50
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_MYCSM30-59
 
  1-
B:30-59
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER_MYCSM39-50
 
  1-
B:39-50

(-) Exons   (0, 0)

(no "Exon" information available for 2V2K)

(-) 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:105
 aligned with FER_MYCSM | P00215 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
            FER_MYCSM     1 TYVIAEPCVDVKDKACIEECPVDCIYEGARMLYIHPDECVDCGACEPVCPVEAIYYEDDVPDQWSSYAQANADFFAELGSPGGASKVGQTDNDPQAIKDLPPQGE 105
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhh....hhhhhhh....eee....eee..........hhhhh....eee.hhhhhhhhhhhhhhhhh........hhhhhh.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------4FE4S_FER_2  PDB: A:30-59     ---------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 ------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2v2k A   1 TYVIAEPCVDVKDKACIEECPVDCIYEGARMLYIHPDECVDcGACEPVCPVEAIYYEDDVPDQWSSYAQANADFFAELGSPGGASKVGQTDNDPQAIKDLPPQGE 105
                                    10        20        30        40 |      50        60        70        80        90       100     
                                                                    42-CSS                                                           

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with FER_MYCSM | P00215 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:103
                                    10        20        30        40        50        60        70        80        90       100   
            FER_MYCSM     1 TYVIAEPCVDVKDKACIEECPVDCIYEGARMLYIHPDECVDCGACEPVCPVEAIYYEDDVPDQWSSYAQANADFFAELGSPGGASKVGQTDNDPQAIKDLPPQ 103
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------Fer4-2v2kB01 B:32-55    ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------Fer4-2v2kB02 B:32-55    ------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eee.hhhh.....hhhhh.....eee....eee..........hhhhh....eee.hhhhhhhhhhhhhhhhh...................hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------4FE4S_FER_2  PDB: B:30-59     -------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 ----------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2v2k B   1 TYVIAEPCVDVKDKACIEECPVDCIYEGARMLYIHPDECVDcGACEPVCPVEAIYYEDDVPDQWSSYAQANADFFAELGSPGGASKVGQTDNDPQAIKDLPPQ 103
                                    10        20        30        40 |      50        60        70        80        90       100   
                                                                    42-CSS                                                         

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2V2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V2K)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: 4Fe-4S (51)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FER_MYCSM | P00215)
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.
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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