PDB entry 2jir

View 2jir on RCSB PDB site
Description: a new catalytic mechanism of periplasmic nitrate reductase from desulfovibrio desulfuricans atcc 27774 from crystallographic and epr data and based on detailed analysis of the sixth ligand
Class: oxidoreductase
Keywords: nitrate assimilation, nitrogenous acceptor, iron, 4fe-4s, transport, molybdenum, periplasmic, disulfide bond, electron transport, iron-sulfur, iron- sulfur, metal-binding, dissimilatory nitrate reductase, molybdopterin cofactor, sulfido ligand, 4fe-4s cluster, oxidoreductase, electron paramagnetic resonance
Deposited on 2007-06-28, released 2008-03-18
The last revision prior to the SCOP 1.75 freeze date was dated 2008-03-18, with a file datestamp of 2008-03-14.
Experiment type: XRAY
Resolution: 2.35 Å
R-factor: 0.16695
AEROSPACI score: 0.44 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: periplasmic nitrate reductase
    Species: Desulfovibrio desulfuricans
    Database cross-references and differences (RAF-indexed):
    • Uniprot P81186 (Start-722)
      • conflict (36)
    Domains in SCOP 1.75: d2jira1, d2jira2
  • Heterogens: CYN, NO2, SF4, MO, MGD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2jirA (A:)
    adnrpekwvkgvcrycgtgcgvlvgvkdgkavaiqgnpnnhnagllclkgsllipvlnsk
    ervtqplvrrhkggklepvswdealdlmasrfrssidmygpnsvawygsgqclteesyva
    nkifkggfgtnnvdgnprlcmasavggyvtsfgkdepmgtyadidqatcffiigsntsea
    hpvlfrriarrkqvepgvkiivadprrtntsriadmhvafrpgtdlafmhsmawviinee
    ldnprfwqryvnfmdaegkpsdfegykaflenyrpekvaeicrvpveqiygaarafaesa
    atmslwcmginqrvqgvfannlihnlhlitgqicrpgatsfsltgqpnacggvrdggals
    hllpagraipnakhraemeklwglpegriapepgyhtvalfealgrgdvkcmiicetnpa
    htlpnlnkvhkamshpesfivcieafpdavtleyadlvlppafwcerdgvygcgerrysl
    tekavdppgqcrptvntlvefarragvdpqlvnfrnaedvwnewrmvskgttydfwgmtr
    erlrkesgliwpcpsedhpgtslryvrgqdpcvpadhpdrfffygkpdgraviwmrpakg
    aaeepdaeyplyltsmrvidhwhtatmtgkvpelqkanpiafveineedaartgikhgds
    vivetrrdamelparvsdvcrpgliavpffdpkklvnklfldatdpvsrepeykicaarv
    rka
    

    Sequence, based on observed residues (ATOM records): (download)
    >2jirA (A:)
    rpekwvkgvcrycgtgcgvlvgvkdgkavaiqgnpnnhnagllclkgsllipvlnskerv
    tqplvrrhkggklepvswdealdlmasrfrssidmygpnsvawygsgqclteesyvanki
    fkggfgtnnvdgnprlcmasavggyvtsfgkdepmgtyadidqatcffiigsntseahpv
    lfrriarrkqvepgvkiivadprrtntsriadmhvafrpgtdlafmhsmawviineeldn
    prfwqryvnfmdaegkpsdfegykaflenyrpekvaeicrvpveqiygaarafaesaatm
    slwcmginqrvqgvfannlihnlhlitgqicrpgatsfsltgqpnacggvrdggalshll
    pagraipnakhraemeklwglpegriapepgyhtvalfealgrgdvkcmiicetnpahtl
    pnlnkvhkamshpesfivcieafpdavtleyadlvlppafwcerdgvygcgerrysltek
    avdppgqcrptvntlvefarragvdpqlvnfrnaedvwnewrmvskgttydfwgmtrerl
    rkesgliwpcpsedhpgtslryvrgqdpcvpadhpdrfffygkpdgraviwmrpakgaae
    epdaeyplyltsmrvidhwhtatmtgkvpelqkanpiafveineedaartgikhgdsviv
    etrrdamelparvsdvcrpgliavpffdpkklvnklfldatdpvsrepeykicaarvrka