PDB entry 2r8z

View 2r8z on RCSB PDB site
Description: Crystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate and a calcium ion
Class: hydrolase
Keywords: YrbI, phosphatase, divalent metal, phosphate, KDO8-P, HAD superfamily, Hydrolase, Lipopolysaccharide biosynthesis, Magnesium
Deposited on 2007-09-11, released 2008-09-23
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.186
AEROSPACI score: 0.44 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8za_
  • Chain 'B':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zb_
  • Chain 'C':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zc_
  • Chain 'D':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zd_
  • Chain 'E':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8ze_
  • Chain 'F':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zf_
  • Chain 'G':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zg_
  • Chain 'H':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zh_
  • Chain 'I':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zi_
  • Chain 'J':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zj_
  • Chain 'K':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zk_
  • Chain 'L':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zl_
  • Chain 'M':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zm_
  • Chain 'N':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zn_
  • Chain 'O':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zo_
  • Chain 'P':
    Compound: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
    Species: Escherichia coli O6 [TaxId:217992]
    Gene: kdsC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2r8zp_
  • Heterogens: CA, PO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2r8zA (A:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zA (A:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2r8zB (B:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zB (B:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2r8zC (C:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zC (C:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2r8zD (D:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zD (D:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2r8zE (E:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zE (E:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakg
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2r8zF (F:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zF (F:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2r8zG (G:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zG (G:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2r8zH (H:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zH (H:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2r8zI (I:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zI (I:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2r8zJ (J:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zJ (J:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2r8zK (K:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zK (K:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >2r8zL (L:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zL (L:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >2r8zM (M:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zM (M:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >2r8zN (N:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zN (N:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >2r8zO (O:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zO (O:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakg
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >2r8zP (P:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8zP (P:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i