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 2.04 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)
    Domains in SCOPe 2.04: d2yfia1, d2yfia2
  • Chain 'B':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: 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)
    Domains in SCOPe 2.04: d2yfic1, d2yfic2
  • Chain 'D':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: 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)
    Domains in SCOPe 2.04: d2yfie1, d2yfie2
  • Chain 'F':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: 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)
    Domains in SCOPe 2.04: d2yfig1, d2yfig2
  • Chain 'H':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: 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)
    Domains in SCOPe 2.04: d2yfii1, d2yfii2
  • Chain 'J':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: 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)
    Domains in SCOPe 2.04: d2yfik1, d2yfik2
  • Chain 'L':
    Compound: Biphenyl dioxygenase subunit beta
    Species: BURKHOLDERIA XENOVORANS [TaxId:266265]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d2yfil_
  • Heterogens: FES, FE2, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

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

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

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

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

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

  • 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