PDB entry 2yfl

View 2yfl on RCSB PDB site
Description: Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran
Class: oxidoreductase
Keywords: oxidoreductase, degradation, bpdo
Deposited on 2011-04-06, released 2012-05-16
The last revision prior to the SCOPe 2.07 freeze date was dated 2012-05-30, with a file datestamp of 2012-05-25.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.2182
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
    Domains in SCOPe 2.07: d2yfla1, d2yfla2
  • Chain 'B':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2yflb_
  • Chain 'C':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
    Domains in SCOPe 2.07: d2yflc1, d2yflc2
  • Chain 'D':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2yfld_
  • Chain 'E':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
    Domains in SCOPe 2.07: d2yfle1, d2yfle2
  • Chain 'F':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2yflf_
  • Chain 'G':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
    Domains in SCOPe 2.07: d2yflg1, d2yflg2
  • Chain 'H':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2yflh_
  • Chain 'I':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
    Domains in SCOPe 2.07: d2yfli1, d2yfli2
  • Chain 'J':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2yflj_
  • Chain 'K':
    Compound: Biphenyl dioxygenase subunit alpha
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P37333 (Start-458)
      • engineered mutation (334-335)
      • engineered mutation (337)
      • engineered mutation (340)
      • engineered mutation (408)
    Domains in SCOPe 2.07: d2yflk1, d2yflk2
  • Chain 'L':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2yfll_
  • Heterogens: FES, FE2, DC4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2yflA (A:)
    mssaikevqgapvkwvtnwtpeairglvdqekglldpriyadqslyelelervfgrswll
    lgheshvpetgdflatymgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftc
    syhgwaydiagklvnvpfekeafcdkkegdcgfdkaewgplqarvatykglvfanwdvqa
    pdletylgdarpymdvmldrtpagtvaiggmqkwvipcnwkfaaeqfcsdmyhagttthl
    sgilagippemdlsqaqiptkgnqfraawgghgsgwyvdepgsllavmgpkvtqywtegp
    aaelaeqrlghtgmpvrrmvgqhmtifptcsflpamnqirvwhprgpneievwaftlvda
    dapaeikeeyrrhnirnfsaggvfeqddgenwveiqkglrgykaksqpfnaqmglgrsqt
    ghpdfpgnvgyvyaeeaargmyhhwmrmmsepswatlkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >2yflA (A:)
    nwtpeairglvdqekglldpriyadqslyelelervfgrswlllgheshvpetgdflaty
    mgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftcsyhgwaydiagklvnvp
    fekeaffdkaewgplqarvatykglvfanwdvqapdletylgdarpymdvmldrtpagtv
    aiggmqkwvipcnwkfaaeqfcsdmyhagttthlsgilagippemdlsqaqiptkgnqfr
    aawgghgsgwyvdepgsllavmgpkvtqywtegpaaelaeqrlghtgmpvrrmvgqhmti
    fptcsflpamnqirvwhprgpneievwaftlvdadapaeikeeyrrhnirnfsaggvfeq
    ddgenwveiqkglrgykaksqpfnaqmglgrsqtghpdfpgnvgyvyaeeaargmyhhwm
    rmmsepswatlkp
    

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

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

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2yflC (C:)
    mssaikevqgapvkwvtnwtpeairglvdqekglldpriyadqslyelelervfgrswll
    lgheshvpetgdflatymgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftc
    syhgwaydiagklvnvpfekeafcdkkegdcgfdkaewgplqarvatykglvfanwdvqa
    pdletylgdarpymdvmldrtpagtvaiggmqkwvipcnwkfaaeqfcsdmyhagttthl
    sgilagippemdlsqaqiptkgnqfraawgghgsgwyvdepgsllavmgpkvtqywtegp
    aaelaeqrlghtgmpvrrmvgqhmtifptcsflpamnqirvwhprgpneievwaftlvda
    dapaeikeeyrrhnirnfsaggvfeqddgenwveiqkglrgykaksqpfnaqmglgrsqt
    ghpdfpgnvgyvyaeeaargmyhhwmrmmsepswatlkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >2yflC (C:)
    nwtpeairglvdqekglldpriyadqslyelelervfgrswlllgheshvpetgdflaty
    mgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftcsyhgwaydiagklvnvp
    fekeaffdkaewgplqarvatykglvfanwdvqapdletylgdarpymdvmldrtpagtv
    aiggmqkwvipcnwkfaaeqfcsdmyhagttthlsgilagippemdlsqaqiptkgnqfr
    aawgghgsgwyvdepgsllavmgpkvtqywtegpaaelaeqrlghtgmpvrrmvgqhmti
    fptcsflpamnqirvwhprgpneievwaftlvdadapaeikeeyrrhnirnfsaggvfeq
    ddgenwveiqkglrgykaksqpfnaqmglgrsqtghpdfpgnvgyvyaeeaargmyhhwm
    rmmsepswatlkp
    

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

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

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2yflE (E:)
    mssaikevqgapvkwvtnwtpeairglvdqekglldpriyadqslyelelervfgrswll
    lgheshvpetgdflatymgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftc
    syhgwaydiagklvnvpfekeafcdkkegdcgfdkaewgplqarvatykglvfanwdvqa
    pdletylgdarpymdvmldrtpagtvaiggmqkwvipcnwkfaaeqfcsdmyhagttthl
    sgilagippemdlsqaqiptkgnqfraawgghgsgwyvdepgsllavmgpkvtqywtegp
    aaelaeqrlghtgmpvrrmvgqhmtifptcsflpamnqirvwhprgpneievwaftlvda
    dapaeikeeyrrhnirnfsaggvfeqddgenwveiqkglrgykaksqpfnaqmglgrsqt
    ghpdfpgnvgyvyaeeaargmyhhwmrmmsepswatlkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >2yflE (E:)
    nwtpeairglvdqekglldpriyadqslyelelervfgrswlllgheshvpetgdflaty
    mgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftcsyhgwaydiagklvnvp
    fekeaffdkaewgplqarvatykglvfanwdvqapdletylgdarpymdvmldrtpagtv
    aiggmqkwvipcnwkfaaeqfcsdmyhagttthlsgilagippemdlsqaqiptkgnqfr
    aawgghgsgwyvdepgsllavmgpkvtqywtegpaaelaeqrlghtgmpvrrmvgqhmti
    fptcsflpamnqirvwhprgpneievwaftlvdadapaeikeeyrrhnirnfsaggvfeq
    ddgenwveiqkglrgykaksqpfnaqmglgrsqtghpdfpgnvgyvyaeeaargmyhhwm
    rmmsepswatlkp
    

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

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

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2yflG (G:)
    mssaikevqgapvkwvtnwtpeairglvdqekglldpriyadqslyelelervfgrswll
    lgheshvpetgdflatymgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftc
    syhgwaydiagklvnvpfekeafcdkkegdcgfdkaewgplqarvatykglvfanwdvqa
    pdletylgdarpymdvmldrtpagtvaiggmqkwvipcnwkfaaeqfcsdmyhagttthl
    sgilagippemdlsqaqiptkgnqfraawgghgsgwyvdepgsllavmgpkvtqywtegp
    aaelaeqrlghtgmpvrrmvgqhmtifptcsflpamnqirvwhprgpneievwaftlvda
    dapaeikeeyrrhnirnfsaggvfeqddgenwveiqkglrgykaksqpfnaqmglgrsqt
    ghpdfpgnvgyvyaeeaargmyhhwmrmmsepswatlkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >2yflG (G:)
    nwtpeairglvdqekglldpriyadqslyelelervfgrswlllgheshvpetgdflaty
    mgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftcsyhgwaydiagklvnvp
    fekeaffdkaewgplqarvatykglvfanwdvqapdletylgdarpymdvmldrtpagtv
    aiggmqkwvipcnwkfaaeqfcsdmyhagttthlsgilagippemdlsqaqiptkgnqfr
    aawgghgsgwyvdepgsllavmgpkvtqywtegpaaelaeqrlghtgmpvrrmvgqhmti
    fptcsflpamnqirvwhprgpneievwaftlvdadapaeikeeyrrhnirnfsaggvfeq
    ddgenwveiqkglrgykaksqpfnaqmglgrsqtghpdfpgnvgyvyaeeaargmyhhwm
    rmmsepswatlkp
    

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

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

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2yflI (I:)
    mssaikevqgapvkwvtnwtpeairglvdqekglldpriyadqslyelelervfgrswll
    lgheshvpetgdflatymgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftc
    syhgwaydiagklvnvpfekeafcdkkegdcgfdkaewgplqarvatykglvfanwdvqa
    pdletylgdarpymdvmldrtpagtvaiggmqkwvipcnwkfaaeqfcsdmyhagttthl
    sgilagippemdlsqaqiptkgnqfraawgghgsgwyvdepgsllavmgpkvtqywtegp
    aaelaeqrlghtgmpvrrmvgqhmtifptcsflpamnqirvwhprgpneievwaftlvda
    dapaeikeeyrrhnirnfsaggvfeqddgenwveiqkglrgykaksqpfnaqmglgrsqt
    ghpdfpgnvgyvyaeeaargmyhhwmrmmsepswatlkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >2yflI (I:)
    nwtpeairglvdqekglldpriyadqslyelelervfgrswlllgheshvpetgdflaty
    mgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftcsyhgwaydiagklvnvp
    fekeaffdkaewgplqarvatykglvfanwdvqapdletylgdarpymdvmldrtpagtv
    aiggmqkwvipcnwkfaaeqfcsdmyhagttthlsgilagippemdlsqaqiptkgnqfr
    aawgghgsgwyvdepgsllavmgpkvtqywtegpaaelaeqrlghtgmpvrrmvgqhmti
    fptcsflpamnqirvwhprgpneievwaftlvdadapaeikeeyrrhnirnfsaggvfeq
    ddgenwveiqkglrgykaksqpfnaqmglgrsqtghpdfpgnvgyvyaeeaargmyhhwm
    rmmsepswatlkp
    

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

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

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2yflK (K:)
    mssaikevqgapvkwvtnwtpeairglvdqekglldpriyadqslyelelervfgrswll
    lgheshvpetgdflatymgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftc
    syhgwaydiagklvnvpfekeafcdkkegdcgfdkaewgplqarvatykglvfanwdvqa
    pdletylgdarpymdvmldrtpagtvaiggmqkwvipcnwkfaaeqfcsdmyhagttthl
    sgilagippemdlsqaqiptkgnqfraawgghgsgwyvdepgsllavmgpkvtqywtegp
    aaelaeqrlghtgmpvrrmvgqhmtifptcsflpamnqirvwhprgpneievwaftlvda
    dapaeikeeyrrhnirnfsaggvfeqddgenwveiqkglrgykaksqpfnaqmglgrsqt
    ghpdfpgnvgyvyaeeaargmyhhwmrmmsepswatlkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >2yflK (K:)
    nwtpeairglvdqekglldpriyadqslyelelervfgrswlllgheshvpetgdflaty
    mgedpvvmvrqkdksikvflnqcrhrgmricrsdagnakaftcsyhgwaydiagklvnvp
    fekeaffdkaewgplqarvatykglvfanwdvqapdletylgdarpymdvmldrtpagtv
    aiggmqkwvipcnwkfaaeqfcsdmyhagttthlsgilagippemdlsqaqiptkgnqfr
    aawgghgsgwyvdepgsllavmgpkvtqywtegpaaelaeqrlghtgmpvrrmvgqhmti
    fptcsflpamnqirvwhprgpneievwaftlvdadapaeikeeyrrhnirnfsaggvfeq
    ddgenwveiqkglrgykaksqpfnaqmglgrsqtghpdfpgnvgyvyaeeaargmyhhwm
    rmmsepswatlkp
    

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

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