PDB entry 2vdh

View 2vdh on RCSB PDB site
Description: crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit c172s mutation
Class: lyase
Keywords: vicinal cysteines, co2/o2 specificity, photosynthesis, transit peptide, photorespiration, metal-binding, hydroxylation, oxidoreductase, methylation, chloroplast, calvin cycle, monooxygenase, lyase, rubisco, plastid, magnesium, acetylation, carbon dioxide fixation
Deposited on 2007-10-09, released 2008-11-04
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.172
AEROSPACI score: 0.4 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdha1, d2vdha2
  • Chain 'B':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhb1, d2vdhb2
  • Chain 'C':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhc1, d2vdhc2
  • Chain 'D':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhd1, d2vdhd2
  • Chain 'E':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhe1, d2vdhe2
  • Chain 'F':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhf1, d2vdhf2
  • Chain 'G':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhg1, d2vdhg2
  • Chain 'H':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00877 (Start-474)
      • conflict (45)
      • engineered mutation (171)
    Domains in SCOPe 2.06: d2vdhh1, d2vdhh2
  • Chain 'I':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhi_
  • Chain 'J':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhj_
  • Chain 'K':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhk_
  • Chain 'L':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhl_
  • Chain 'M':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhm_
  • Chain 'N':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhn_
  • Chain 'O':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdho_
  • Chain 'P':
    Compound: ribulose bisphosphate carboxylase small chain 1
    Species: CHLAMYDOMONAS REINHARDTII [TaxId:3055]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vdhp_
  • Heterogens: MG, CAP, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2vdhA (A:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhA (A:)
    agfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwttvw
    tdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfkal
    ralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygravy
    eclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtceem
    mkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhgih
    frvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdwcs
    mpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleactqa
    rnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2vdhB (B:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhB (B:)
    kagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwt
    tvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgf
    kalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygr
    avyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtc
    eemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnh
    gihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqd
    wcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleac
    tqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2vdhC (C:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhC (C:)
    agagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwtt
    vwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfk
    alralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtce
    emmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhg
    ihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdw
    csmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleact
    qarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2vdhD (D:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhD (D:)
    agfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwttvw
    tdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfkal
    ralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygravy
    eclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtceem
    mkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhgih
    frvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdwcs
    mpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleactqa
    rnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2vdhE (E:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhE (E:)
    agfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwttvw
    tdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfkal
    ralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygravy
    eclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtceem
    mkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhgih
    frvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdwcs
    mpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleactqa
    rnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2vdhF (F:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhF (F:)
    agagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwtt
    vwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfk
    alralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtce
    emmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhg
    ihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdw
    csmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleact
    qarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2vdhG (G:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhG (G:)
    agagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwtt
    vwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfk
    alralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtce
    emmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhg
    ihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdw
    csmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleact
    qarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2vdhH (H:)
    mvpqtetkagagfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaae
    sstgtwttvwtdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsi
    vgnvfgfkalralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghyl
    natagtceemmkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhav
    idrqrnhgihfrvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsr
    giyftqdwcsmpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaan
    rvaleactqarnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vdhH (H:)
    agfkagvkdyrltyytpdyvvrdtdilaafrmtpqpgvppeecgaavaaesstgtwttvw
    tdgltsldrykgrcydiepvpgednqyiayvaypidlfeegsvtnmftsivgnvfgfkal
    ralrledlrippayvktfvgpphgiqverdklnkygrgllgstikpklglsaknygravy
    eclrggldftkddenvnsqpfmrwrdrflfvaeaiykaqaetgevkghylnatagtceem
    mkravcakelgvpiimhdyltggftantslaiycrdnglllhihramhavidrqrnhgih
    frvlakalrmsggdhlhsgtvvgklegerevtlgfvdlmrddyvekdrsrgiyftqdwcs
    mpgvmpvasggihvwhmpalveifgddaclqfgggtlghpwgnapgaaanrvaleactqa
    rnegrdlareggdvirsackwspelaaacevwkeikfefdtidkl
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhI (I:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhJ (J:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhK (K:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhL (L:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhM (M:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhN (N:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhO (O:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vdhP (P:)
    mmvwtpvnnkmfetfsylppltdeqiaaqvdyivangwipclefaeadkayvsnesairf
    gsvsclyydnrywtmwklpmfgcrdpmqvlreivactkafpdayvrlvafdnqkqvqimg
    flvqrpktardfqpankrsv