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(-) Description

Title :  CRYSTAL STRUCTURE OF [2FE-2S] FERREDOXIN ARX FROM NOVOSPHINGOBIUM AROMATICIVORANS
 
Authors :  W. Yang, S. G. Bell, H. Wang, M. Bartlam, L. L. Wong, Z. Rao
Date :  25 Feb 10  (Deposition) - 23 Jun 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  [2Fe-2S] Ferredoxin, Iron, Iron-Sulfur, Metal-Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Yang, S. G. Bell, H. Wang, W. Zhou, N. Hoskins, A. Dale, M. Bartlam, L. L. Wong, Z. Rao
Molecular Characterization Of A Class I P450 Electron Transfer System From Novosphingobium Aromaticivorans Dsm12444
J. Biol. Chem. V. 285 27372 2010
PubMed-ID: 20576606  |  Reference-DOI: 10.1074/JBC.M110.118349

(-) Compounds

Molecule 1 - FERREDOXIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 17-120
    Gene: SARO_1477
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444
    Synonym: [2FE-2S] FERREDOXIN ARX

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1FES5Ligand/IonFE2/S2 (INORGANIC) CLUSTER
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1FES10Ligand/IonFE2/S2 (INORGANIC) CLUSTER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:38 , CYS A:40 , GLY A:42 , CYS A:44 , SER A:45 , CYS A:46 , CYS A:49 , CYS A:86BINDING SITE FOR RESIDUE FES A 500
2AC2SOFTWARECYS B:40 , GLY B:42 , CYS B:44 , SER B:45 , CYS B:46 , CYS B:49 , CYS B:86BINDING SITE FOR RESIDUE FES B 500
3AC3SOFTWARECYS C:40 , GLY C:42 , CYS C:44 , SER C:45 , CYS C:46 , CYS C:49 , CYS C:86BINDING SITE FOR RESIDUE FES C 500
4AC4SOFTWAREALA D:38 , CYS D:40 , GLY D:42 , CYS D:44 , SER D:45 , CYS D:46 , CYS D:49 , CYS D:86BINDING SITE FOR RESIDUE FES D 500
5AC5SOFTWARECYS E:40 , GLY E:42 , CYS E:44 , SER E:45 , CYS E:46 , CYS E:49 , CYS E:86BINDING SITE FOR RESIDUE FES E 500

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:43 -A:43
2B:43 -D:43
3C:43 -E:43

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LXF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LXF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LXF)

(-) Exons   (0, 0)

(no "Exon" information available for 3LXF)

(-) 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:104
 aligned with Q2G8A3_NOVAD | Q2G8A3 from UniProtKB/TrEMBL  Length:120

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
         Q2G8A3_NOVAD    17 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 120
               SCOP domains d3lxfa_ A: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee.hhhhhhh...hhhhhhhhhh.......eee.hhh..hhhhh..eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3lxf A   2 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 105
                                    11        21        31        41        51        61        71        81        91       101    


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with Q2G8A3_NOVAD | Q2G8A3 from UniProtKB/TrEMBL  Length:120

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
         Q2G8A3_NOVAD    17 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 120
               SCOP domains d3lxfb_ B: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee.hhhhhhh...hhhhhhhhhh.......eee.hhh..hhhhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3lxf B   2 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 105
                                    11        21        31        41        51        61        71        81        91       101    


Chain C from PDB  Type:PROTEIN  Length:104
 aligned with Q2G8A3_NOVAD | Q2G8A3 from UniProtKB/TrEMBL  Length:120

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
         Q2G8A3_NOVAD    17 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 120
               SCOP domains d3lxfc_ C: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee.hhhhhhh...hhhhhhhhhh.......eee.hhh..hhhhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3lxf C   2 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 105
                                    11        21        31        41        51        61        71        81        91       101    


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with Q2G8A3_NOVAD | Q2G8A3 from UniProtKB/TrEMBL  Length:120

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
         Q2G8A3_NOVAD    17 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 120
               SCOP domains d3lxfd_ D: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee.hhhhhhh...hhhhhhhhhh.......eee.hhh..hhhhh..eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3lxf D   2 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 105
                                    11        21        31        41        51        61        71        81        91       101    


Chain E from PDB  Type:PROTEIN  Length:104
 aligned with Q2G8A3_NOVAD | Q2G8A3 from UniProtKB/TrEMBL  Length:120

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
         Q2G8A3_NOVAD    17 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 120
               SCOP domains d3lxfe_ E: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Fer2-3lxfE01 E:7-91                                                                  -------------- Pfam domains (1)
           Pfam domains (2) -----Fer2-3lxfE02 E:7-91                                                                  -------------- Pfam domains (2)
           Pfam domains (3) -----Fer2-3lxfE03 E:7-91                                                                  -------------- Pfam domains (3)
           Pfam domains (4) -----Fer2-3lxfE04 E:7-91                                                                  -------------- Pfam domains (4)
           Pfam domains (5) -----Fer2-3lxfE05 E:7-91                                                                  -------------- Pfam domains (5)
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhh..................eeee.hhhhhhh...hhhhhhhhhh.......eee.hhh..hhhhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3lxf E   2 TAILVTTRDGTRTEIQAEPGLSLMEALRDAGIDELLALCGGCCSCATCHVLVAPAFADRLPALSGDENDLLDSSDHRTPHSRLSCQITINDKLEGLEVEIAPED 105
                                    11        21        31        41        51        61        71        81        91       101
   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, 5)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LXF)

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: Fer2 (69)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q2G8A3_NOVAD | Q2G8A3)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two 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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

3lxd ASSOCIATE FERREDOXIN REDUCTASE ARR FROM NOVOSPHINGOBIUM AROMATICIVORANS
3lxh CRYSTAL STRUCTURE OF NATIVE CYTOCHROME P450 CYP101D1
3lxi CRYSTAL STRUCTURE OF CAMPHOR-BOUND CYP101D1