PDB entry 2r8e

View 2r8e on RCSB PDB site
Description: Crystal structure of YrbI from Escherichia coli in complex with Mg
Class: hydrolase
Keywords: Phosphatase, YrbI, divalent metal, HAD superfamily, KDO 8-P, Hydrolase, Lipopolysaccharide biosynthesis, Magnesium
Deposited on 2007-09-10, released 2008-09-23
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-11-03, with a file datestamp of 2009-10-30.
Experiment type: XRAY
Resolution: 1.4 Å
R-factor: 0.16
AEROSPACI score: 0.7 (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: d2r8ea_
  • 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: d2r8eb_
  • 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: d2r8ec_
  • 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: d2r8ed_
  • 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: d2r8ee_
  • 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: d2r8ef_
  • 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: d2r8eg_
  • 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: d2r8eh_
  • Heterogens: MG, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2r8eA (A:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eA (A:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2r8eB (B:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eB (B:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2r8eC (C:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eC (C:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2r8eD (D:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eD (D:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2r8eE (E:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eE (E:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2r8eF (F:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eF (F:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2r8eG (G:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eG (G:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2r8eH (H:)
    mskagaslatcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgy
    gircaltsdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenv
    ayvgddlidwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkl
    deakgqsi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2r8eH (H:)
    latcygpvsadvmakaenirllildvdgvlsdgliymgnngeelkafnvrdgygircalt
    sdievaiitgrkaklvedrcatlgithlyqgqsnkliafsdlleklaiapenvayvgddl
    idwpvmekvglsvavadahpllipradyvtriaggrgavrevcdllllaqgkldeakgqs
    i