PDB entry 3myr

View 3myr on RCSB PDB site
Description: Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state
Class: oxidoreductase
Keywords: [NiFe] hydrogenase, Allochromatium vinosum, photosynthetic purple-sulfur bacterium, iron-sulfur cluster, Ni-A state, OXIDOREDUCTASE
Deposited on 2010-05-11, released 2010-08-04
The last revision prior to the SCOPe 2.07 freeze date was dated 2010-10-06, with a file datestamp of 2010-10-01.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.14
AEROSPACI score: 0.46 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myra_
  • Chain 'B':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myrb_
  • Chain 'C':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myrc_
  • Chain 'D':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myrd_
  • Chain 'E':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myre_
  • Chain 'F':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myrf_
  • Chain 'G':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myrg_
  • Chain 'H':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Allochromatium vinosum [TaxId:1049]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3myrh_
  • Heterogens: SF4, F3S, IMD, CL, NFV, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3myrA (A:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvpl
    

    Sequence, based on observed residues (ATOM records): (download)
    >3myrA (A:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3myrB (B:)
    mserivvdpitrieghlrieaqmdgatiaqayssgtmvrgietilkgrdprdawafvqri
    cgvctlvhgiasvravedalrielplnaqlirnlmigaqyihdhvmhfyhlhaldwvdvv
    salsadpratselaqsisawpksspgyfadtqkriktfvesgqlgifangywghpayrlp
    peanlmavahylealawqrdtakfhaifggknphpnfvvggvpspidldsdsalnakrla
    evrnliqsmrtfvdqvyvpdtlaiagfykdwgergeglgnflcygdlptgasldpatflf
    prgaildrdlstihevdleatgeiqefvnhswyeysvgndrglhpyegqtnleydrrggv
    appykqldvsdgyswlkaprwkgrsvevgplarvlmlyatghdqarelvdstlsrldlpv
    dalystlgrtaaraleskilvdamqgwydglianvksgdtktfnetlwepsswpsraqgv
    gimeaprgalghwiviedgrianyqavvpstwnagprdgrgqagayeaalqdnhqlvdvk
    qpieilrtihsfdpciacavh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3myrB (B:)
    erivvdpitrieghlrieaqmdgatiaqayssgtmvrgietilkgrdprdawafvqricg
    vctlvhgiasvravedalrielplnaqlirnlmigaqyihdhvmhfyhlhaldwvdvvsa
    lsadpratselaqsisawpksspgyfadtqkriktfvesgqlgifangywghpayrlppe
    anlmavahylealawqrdtakfhaifggknphpnfvvggvpspidldsdsalnakrlaev
    rnliqsmrtfvdqvyvpdtlaiagfykdwgergeglgnflcygdlptgasldpatflfpr
    gaildrdlstihevdleatgeiqefvnhswyeysvgndrglhpyegqtnleydrrggvap
    pykqldvsdgyswlkaprwkgrsvevgplarvlmlyatghdqarelvdstlsrldlpvda
    lystlgrtaaraleskilvdamqgwydglianvksgdtktfnetlwepsswpsraqgvgi
    meaprgalghwiviedgrianyqavvpstwnagprdgrgqagayeaalqdnhqlvdvkqp
    ieilrtihsfdpciacavh
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3myrC (C:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvpl
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3myrD (D:)
    mserivvdpitrieghlrieaqmdgatiaqayssgtmvrgietilkgrdprdawafvqri
    cgvctlvhgiasvravedalrielplnaqlirnlmigaqyihdhvmhfyhlhaldwvdvv
    salsadpratselaqsisawpksspgyfadtqkriktfvesgqlgifangywghpayrlp
    peanlmavahylealawqrdtakfhaifggknphpnfvvggvpspidldsdsalnakrla
    evrnliqsmrtfvdqvyvpdtlaiagfykdwgergeglgnflcygdlptgasldpatflf
    prgaildrdlstihevdleatgeiqefvnhswyeysvgndrglhpyegqtnleydrrggv
    appykqldvsdgyswlkaprwkgrsvevgplarvlmlyatghdqarelvdstlsrldlpv
    dalystlgrtaaraleskilvdamqgwydglianvksgdtktfnetlwepsswpsraqgv
    gimeaprgalghwiviedgrianyqavvpstwnagprdgrgqagayeaalqdnhqlvdvk
    qpieilrtihsfdpciacavh
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3myrE (E:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvpl
    

    Sequence, based on observed residues (ATOM records): (download)
    >3myrE (E:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvp
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3myrF (F:)
    mserivvdpitrieghlrieaqmdgatiaqayssgtmvrgietilkgrdprdawafvqri
    cgvctlvhgiasvravedalrielplnaqlirnlmigaqyihdhvmhfyhlhaldwvdvv
    salsadpratselaqsisawpksspgyfadtqkriktfvesgqlgifangywghpayrlp
    peanlmavahylealawqrdtakfhaifggknphpnfvvggvpspidldsdsalnakrla
    evrnliqsmrtfvdqvyvpdtlaiagfykdwgergeglgnflcygdlptgasldpatflf
    prgaildrdlstihevdleatgeiqefvnhswyeysvgndrglhpyegqtnleydrrggv
    appykqldvsdgyswlkaprwkgrsvevgplarvlmlyatghdqarelvdstlsrldlpv
    dalystlgrtaaraleskilvdamqgwydglianvksgdtktfnetlwepsswpsraqgv
    gimeaprgalghwiviedgrianyqavvpstwnagprdgrgqagayeaalqdnhqlvdvk
    qpieilrtihsfdpciacavh
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3myrG (G:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvpl
    

    Sequence, based on observed residues (ATOM records): (download)
    >3myrG (G:)
    arrpsviwlsfqectgctesltrahaptledlildfisldyhhtlqaasgeaaeaarlqa
    mdenrgqylvivdgsipgpdanpgfstvaghsnysilmetvehaaaviavgtcaafgglp
    qarpnptgamsvmdlvrdkpvinvpgcppipmvitgviahylvfgrlpeldgygrplafy
    gqsihdrcyrrpfydkglfaesfddegakqgwclyrlgckgpttynacatmkwndgtswp
    veaghpclgcsepqfwdaggfyepvsvp
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3myrH (H:)
    mserivvdpitrieghlrieaqmdgatiaqayssgtmvrgietilkgrdprdawafvqri
    cgvctlvhgiasvravedalrielplnaqlirnlmigaqyihdhvmhfyhlhaldwvdvv
    salsadpratselaqsisawpksspgyfadtqkriktfvesgqlgifangywghpayrlp
    peanlmavahylealawqrdtakfhaifggknphpnfvvggvpspidldsdsalnakrla
    evrnliqsmrtfvdqvyvpdtlaiagfykdwgergeglgnflcygdlptgasldpatflf
    prgaildrdlstihevdleatgeiqefvnhswyeysvgndrglhpyegqtnleydrrggv
    appykqldvsdgyswlkaprwkgrsvevgplarvlmlyatghdqarelvdstlsrldlpv
    dalystlgrtaaraleskilvdamqgwydglianvksgdtktfnetlwepsswpsraqgv
    gimeaprgalghwiviedgrianyqavvpstwnagprdgrgqagayeaalqdnhqlvdvk
    qpieilrtihsfdpciacavh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3myrH (H:)
    erivvdpitrieghlrieaqmdgatiaqayssgtmvrgietilkgrdprdawafvqricg
    vctlvhgiasvravedalrielplnaqlirnlmigaqyihdhvmhfyhlhaldwvdvvsa
    lsadpratselaqsisawpksspgyfadtqkriktfvesgqlgifangywghpayrlppe
    anlmavahylealawqrdtakfhaifggknphpnfvvggvpspidldsdsalnakrlaev
    rnliqsmrtfvdqvyvpdtlaiagfykdwgergeglgnflcygdlptgasldpatflfpr
    gaildrdlstihevdleatgeiqefvnhswyeysvgndrglhpyegqtnleydrrggvap
    pykqldvsdgyswlkaprwkgrsvevgplarvlmlyatghdqarelvdstlsrldlpvda
    lystlgrtaaraleskilvdamqgwydglianvksgdtktfnetlwepsswpsraqgvgi
    meaprgalghwiviedgrianyqavvpstwnagprdgrgqagayeaalqdnhqlvdvkqp
    ieilrtihsfdpciacavh