PDB entry 2yfi

View 2yfi on RCSB PDB site
Description: crystal structure of biphenyl dioxygenase variant rr41 (bpdo-rr41)
Class: oxidoreductase
Keywords: oxidoreductase, degradation
Deposited on 2011-04-06, released 2011-06-08
The last revision prior to the SCOPe 2.02 freeze date was dated 2011-08-10, with a file datestamp of 2011-08-05.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: 0.20152
AEROSPACI score: 0.41 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
  • Chain 'B':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d2yfib_
  • Chain 'C':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
  • Chain 'D':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d2yfid_
  • Chain 'E':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
  • Chain 'F':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d2yfif_
  • Chain 'G':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
  • Chain 'H':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d2yfih_
  • Chain 'I':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
  • Chain 'J':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d2yfij_
  • Chain 'K':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
  • Chain 'L':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d2yfil_
  • Heterogens: FES, FE2, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2yfiB (B:)
mtnpsphffktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmpl
rtnrmiregeleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivk
etatpdtfevnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastll
snnlsmff

    Sequence, based on observed residues (ATOM records): (download) 
    >2yfiB (B:)
fktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmplrtnrmire
geleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivketatpdtf
evnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastllsnnlsmff

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2yfiD (D:)
mtnpsphffktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmpl
rtnrmiregeleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivk
etatpdtfevnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastll
snnlsmff

    Sequence, based on observed residues (ATOM records): (download) 
    >2yfiD (D:)
fktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmplrtnrmire
geleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivketatpdtf
evnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastllsnnlsmff

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >2yfiF (F:)
mtnpsphffktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmpl
rtnrmiregeleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivk
etatpdtfevnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastll
snnlsmff

    Sequence, based on observed residues (ATOM records): (download) 
    >2yfiF (F:)
fktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmplrtnrmire
geleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivketatpdtf
evnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastllsnnlsmff

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >2yfiH (H:)
mtnpsphffktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmpl
rtnrmiregeleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivk
etatpdtfevnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastll
snnlsmff

    Sequence, based on observed residues (ATOM records): (download) 
    >2yfiH (H:)
fktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmplrtnrmire
geleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivketatpdtf
evnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastllsnnlsmff

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >2yfiJ (J:)
mtnpsphffktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmpl
rtnrmiregeleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivk
etatpdtfevnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastll
snnlsmff

    Sequence, based on observed residues (ATOM records): (download) 
    >2yfiJ (J:)
fktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmplrtnrmire
geleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivketatpdtf
evnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastllsnnlsmff

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >2yfiL (L:)
mtnpsphffktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmpl
rtnrmiregeleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivk
etatpdtfevnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastll
snnlsmff

    Sequence, based on observed residues (ATOM records): (download) 
    >2yfiL (L:)
fktfewpskaaglelqneieqfyyreaqlldhrayeawfalldkdihyfmplrtnrmire
geleysgdqdlahfdethetmygrirkvtsdvgwaenppsrtrhlvsnvivketatpdtf
evnsafilyrnrlerqvdifagerrdvlrradnnlgfsiakrtilldastllsnnlsmff