PDB entry 4iy7

View 4iy7 on RCSB PDB site
Description: crystal structure of cystathionine gamma lyase (XometC) from Xanthomonas oryzae pv. oryzae in complex with E-site serine, A-site external aldimine structure with serine and A-site external aldimine structure with aminoacrylate intermediates
Class: lyase
Keywords: XOCGL, SERINE EXTERNAL SCHIFF BASE, AMINOACRYLATE EXTERNAL SCHIFF BASE, PLP DEPENDENT ENZYME, LYASE, Cys-Met metabolism PLP dependent enzyme, cystathionine gamma lyase, PLP binding
Deposited on 2013-01-28, released 2014-01-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-02-26, with a file datestamp of 2014-02-21.
Experiment type: XRAY
Resolution: 1.7 Å
R-factor: 0.136
AEROSPACI score: 0.51 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Cystathionine gamma-lyase-like protein
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iy7a_
  • Chain 'B':
    Compound: Cystathionine gamma-lyase-like protein
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iy7b_
  • Chain 'C':
    Compound: Cystathionine gamma-lyase-like protein
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iy7c_
  • Chain 'D':
    Compound: Cystathionine gamma-lyase-like protein
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iy7d_
  • Heterogens: SER, GOL, SO4, 0JO, PYR, KOU, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4iy7A (A:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iy7A (A:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralv
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4iy7B (B:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iy7B (B:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralv
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4iy7C (C:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iy7C (C:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralv
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4iy7D (D:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iy7D (D:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralvnq