PDB entry 2gbx

View 2gbx on RCSB PDB site
Description: Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to Biphenyl
Class: oxidoreductase
Keywords: rieske oxygenase, oxidoreductase, non heme iron, dioxygenase
Deposited on 2006-03-12, released 2007-03-20
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.238
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Biphenyl 2,3-Dioxygenase Alpha Subunit
    Species: Sphingobium yanoikuyae [TaxId:13690]
    Gene: bphA1fA2f
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2gbxa1, d2gbxa2
  • Chain 'B':
    Compound: Biphenyl 2,3-Dioxygenase Beta Subunit
    Species: Sphingobium yanoikuyae [TaxId:13690]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2gbxb_
  • Chain 'C':
    Compound: Biphenyl 2,3-Dioxygenase Alpha Subunit
    Species: Sphingobium yanoikuyae [TaxId:13690]
    Gene: bphA1fA2f
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2gbxc1, d2gbxc2
  • Chain 'D':
    Compound: Biphenyl 2,3-Dioxygenase Beta Subunit
    Species: Sphingobium yanoikuyae [TaxId:13690]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2gbxd_
  • Chain 'E':
    Compound: Biphenyl 2,3-Dioxygenase Alpha Subunit
    Species: Sphingobium yanoikuyae [TaxId:13690]
    Gene: bphA1fA2f
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2gbxe1, d2gbxe2
  • Chain 'F':
    Compound: Biphenyl 2,3-Dioxygenase Beta Subunit
    Species: Sphingobium yanoikuyae [TaxId:13690]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2gbxf_
  • Heterogens: FE, ZN, FES, BNL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2gbxA (A:)
    mssdatlvdtvnasqsrqvfwdedvyaleierifsrawlmlgheslvpkpgdfittymae
    dkvilshqsdgtfrafinscshrgnqichadsgnakafvcnyhgwvfgqdgslvdvples
    rcyhnsldkqklaaksvrvetykgfifgchdpeapsledylgefryyldtiwegagggme
    llgppmksllqcnwkvpaenfigdgyhvgwthaaalsqiggelaglagnradipfddlgl
    qfttrhghgfgvidnaaaglhikregwtkfledtrgevrrkfgpererlylghwncsifp
    ncsflygtntfkiwhprgpheievwtytivprdadpatksmiqreairtfgtagtlesdd
    genmssatyinrgvitrngrmnstmgvgyegphpvypgivgisfigetsyrgfyrfwkem
    idapdwasvkanddtwdsvfpnrnfwneklnaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >2gbxA (A:)
    tlvdtvnasqsrqvfwdedvyaleierifsrawlmlgheslvpkpgdfittymaedkvil
    shqsdgtfrafinscshrgnqichadsgnakafvcnyhgwvfgqdgslvdvplesrcyhn
    sldkqklaaksvrvetykgfifgchdpeapsledylgefryyldtiwegagggmellgpp
    mksllqcnwkvpaenfigdgyhvgwthaaalsqiggelaglagnradipfddlglqfttr
    hghgfgvidnaaaglhikregwtkfledtrgevrrkfgpererlylghwncsifpncsfl
    ygtntfkiwhprgpheievwtytivprdadpatksmiqreairtfgtagtlesddgenms
    satyinrgvitrngrmnstmgvgyegphpvypgivgisfigetsyrgfyrfwkemidapd
    wasvkanddtwdsvfpnrnfwneklnaae
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2gbxB (B:)
    msseqipvtpdvhydieahyraevrmfqtgqyrewlqgmvaedihywmpiyeqrltrdrr
    pdptpddaaiynddfgelkqrverlysgqvwmedppskiryfvsnveafeagngeldvls
    nilvyrnrrqtevtvhtlgredklrrdgngfkvfrrklildarvtqdknlyffc
    

    Sequence, based on observed residues (ATOM records): (download)
    >2gbxB (B:)
    qipvtpdvhydieahyraevrmfqtgqyrewlqgmvaedihywmpiyeqrltrdrrpdpt
    pddaaiynddfgelkqrverlysgqvwmedppskiryfvsnveafeagngeldvlsnilv
    yrnrrqtevtvhtlgredklrrdgngfkvfrrklildarvtqdknlyffc
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2gbxC (C:)
    mssdatlvdtvnasqsrqvfwdedvyaleierifsrawlmlgheslvpkpgdfittymae
    dkvilshqsdgtfrafinscshrgnqichadsgnakafvcnyhgwvfgqdgslvdvples
    rcyhnsldkqklaaksvrvetykgfifgchdpeapsledylgefryyldtiwegagggme
    llgppmksllqcnwkvpaenfigdgyhvgwthaaalsqiggelaglagnradipfddlgl
    qfttrhghgfgvidnaaaglhikregwtkfledtrgevrrkfgpererlylghwncsifp
    ncsflygtntfkiwhprgpheievwtytivprdadpatksmiqreairtfgtagtlesdd
    genmssatyinrgvitrngrmnstmgvgyegphpvypgivgisfigetsyrgfyrfwkem
    idapdwasvkanddtwdsvfpnrnfwneklnaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >2gbxC (C:)
    tlvdtvnasqsrqvfwdedvyaleierifsrawlmlgheslvpkpgdfittymaedkvil
    shqsdgtfrafinscshrgnqichadsgnakafvcnyhgwvfgqdgslvdvplesrcyhn
    sldkqklaaksvrvetykgfifgchdpeapsledylgefryyldtiwegagggmellgpp
    mksllqcnwkvpaenfigdgyhvgwthaaalsqiggelaglagnradipfddlglqfttr
    hghgfgvidnaaaglhikregwtkfledtrgevrrkfgpererlylghwncsifpncsfl
    ygtntfkiwhprgpheievwtytivprdadpatksmiqreairtfgtagtlesddgenms
    satyinrgvitrngrmnstmgvgyegphpvypgivgisfigetsyrgfyrfwkemidapd
    wasvkanddtwdsvfpnrnfwnekln
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2gbxD (D:)
    msseqipvtpdvhydieahyraevrmfqtgqyrewlqgmvaedihywmpiyeqrltrdrr
    pdptpddaaiynddfgelkqrverlysgqvwmedppskiryfvsnveafeagngeldvls
    nilvyrnrrqtevtvhtlgredklrrdgngfkvfrrklildarvtqdknlyffc
    

    Sequence, based on observed residues (ATOM records): (download)
    >2gbxD (D:)
    qipvtpdvhydieahyraevrmfqtgqyrewlqgmvaedihywmpiyeqrltrdrrpdpt
    pddaaiynddfgelkqrverlysgqvwmedppskiryfvsnveafeagngeldvlsnilv
    yrnrrqtevtvhtlgredklrrdgngfkvfrrklildarvtqdknlyffc
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2gbxE (E:)
    mssdatlvdtvnasqsrqvfwdedvyaleierifsrawlmlgheslvpkpgdfittymae
    dkvilshqsdgtfrafinscshrgnqichadsgnakafvcnyhgwvfgqdgslvdvples
    rcyhnsldkqklaaksvrvetykgfifgchdpeapsledylgefryyldtiwegagggme
    llgppmksllqcnwkvpaenfigdgyhvgwthaaalsqiggelaglagnradipfddlgl
    qfttrhghgfgvidnaaaglhikregwtkfledtrgevrrkfgpererlylghwncsifp
    ncsflygtntfkiwhprgpheievwtytivprdadpatksmiqreairtfgtagtlesdd
    genmssatyinrgvitrngrmnstmgvgyegphpvypgivgisfigetsyrgfyrfwkem
    idapdwasvkanddtwdsvfpnrnfwneklnaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >2gbxE (E:)
    tlvdtvnasqsrqvfwdedvyaleierifsrawlmlgheslvpkpgdfittymaedkvil
    shqsdgtfrafinscshrgnqichadsgnakafvcnyhgwvfgqdgslvdvplesrcyhn
    sldkqklaaksvrvetykgfifgchdpeapsledylgefryyldtiwegagggmellgpp
    mksllqcnwkvpaenfigdgyhvgwthaaalsqiggelaglagnradipfddlglqfttr
    hghgfgvidnaaaglhikregwtkfledtrgevrrkfgpererlylghwncsifpncsfl
    ygtntfkiwhprgpheievwtytivprdadpatksmiqreairtfgtagtlesddgenms
    satyinrgvitrngrmnstmgvgyegphpvypgivgisfigetsyrgfyrfwkemidapd
    wasvkanddtwdsvfpnrnfwneklnaae
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2gbxF (F:)
    msseqipvtpdvhydieahyraevrmfqtgqyrewlqgmvaedihywmpiyeqrltrdrr
    pdptpddaaiynddfgelkqrverlysgqvwmedppskiryfvsnveafeagngeldvls
    nilvyrnrrqtevtvhtlgredklrrdgngfkvfrrklildarvtqdknlyffc
    

    Sequence, based on observed residues (ATOM records): (download)
    >2gbxF (F:)
    qipvtpdvhydieahyraevrmfqtgqyrewlqgmvaedihywmpiyeqrltrdrrpdpt
    pddaaiynddfgelkqrverlysgqvwmedppskiryfvsnveafeagngeldvlsnilv
    yrnrrqtevtvhtlgredklrrdgngfkvfrrklildarvtqdknlyffc