PDB entry 5kaf

View 5kaf on RCSB PDB site
Description: RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution
Class: electron transport
Keywords: photosystems, transmembrane, room temperature, electron transport
Deposited on 2016-06-01, released 2016-11-23
The last revision prior to the SCOPe 2.06 freeze date was dated 2016-11-23, with a file datestamp of 2016-11-18.
Experiment type: XRAY
Resolution: 3 Å
R-factor: N/A
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Photosystem II protein D1 1
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A444 (Start-343)
• Chain 'B':
  Compound: Photosystem II CP47 reaction center protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIQ1
• Chain 'C':
  Compound: Photosystem II CP43 reaction center protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIF8 (Start-460)
• Chain 'D':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8CM25 (Start-351)
• Chain 'E':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIP0 (Start-83)
• Chain 'F':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIN9 (Start-44)
• Chain 'H':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DJ43
• Chain 'I':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DJZ6 (1-End)
    • expression tag (0)
• Chain 'J':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P59087 (Start-39)
• Chain 'K':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q9F1K9 (Start-45)
• Chain 'L':
  Compound: Photosystem II reaction center protein L
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIN8 (0-36)
• Chain 'M':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DHA7 (1-End)
    • expression tag (0)
  Domains in SCOPe 2.06: d5kafm1, d5kafm2
• Chain 'O':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A431 (Start-271)
• Chain 'R':
  Compound: Photosystem II protein Y
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DKM3
• Chain 'T':
  Compound: Photosystem II reaction center protein T
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIQ0 (1-End)
    • expression tag (0)
• Chain 'U':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q9F1L5 (Start-133)
• Chain 'V':
  Compound: cytochrome c-550
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A386 (Start-162)
• Chain 'X':
  Compound: Photosystem II reaction center X protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q9F1R6
• Chain 'Y':
  Compound: Photosystem II reaction center protein ycf12
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DJI1 (Start-45)
• Chain 'Z':
  Compound: Photosystem II reaction center protein Z
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DHJ2 (0-61)
• Chain 'a':
  Compound: Photosystem II protein D1 1
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A444 (Start-343)
• Chain 'b':
  Compound: Photosystem II CP47 reaction center protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIQ1
• Chain 'c':
  Compound: Photosystem II CP43 reaction center protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIF8 (Start-460)
• Chain 'd':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8CM25 (Start-351)
• Chain 'e':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIP0 (Start-83)
• Chain 'f':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIN9 (Start-44)
  Domains in SCOPe 2.06: d5kaff_
• Chain 'h':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DJ43
• Chain 'i':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DJZ6 (1-End)
    • expression tag (0)
• Chain 'j':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P59087 (Start-39)
• Chain 'k':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q9F1K9 (Start-45)
• Chain 'l':
  Compound: Photosystem II reaction center protein L
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIN8 (0-36)
  Domains in SCOPe 2.06: d5kafl_
• Chain 'm':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DHA7 (1-End)
    • expression tag (0)
• Chain 'o':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A431 (Start-271)
  Domains in SCOPe 2.06: d5kafo_
• Chain 'r':
  Compound: Photosystem II protein Y
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DKM3
• Chain 't':
  Compound: Photosystem II reaction center protein T
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DIQ0 (1-End)
    • expression tag (0)
• Chain 'u':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q9F1L5 (Start-133)
• Chain 'v':
  Compound: cytochrome c-550
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A386 (Start-162)
• Chain 'x':
  Compound: Photosystem II reaction center X protein
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q9F1R6
• Chain 'y':
  Compound: Photosystem II reaction center protein ycf12
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DJI1 (Start-45)
• Chain 'z':
  Compound: Photosystem II reaction center protein Z
  Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q8DHJ2 (0-61)
• Heterogens: OEX, FE2, SQD, CL, CLA, PHO, BCR, PL9, LMG, UNL, LHG, BCT, DGD, HEM, HOH

PDB Chain Sequences:

• Chain 'A':
  No sequence available.
  
  
• Chain 'B':
  No sequence available.
  
  
• Chain 'C':
  No sequence available.
  
  
• Chain 'D':
  No sequence available.
  
  
• Chain 'E':
  No sequence available.
  
  
• Chain 'F':
  No sequence available.
  
  
• Chain 'H':
  No sequence available.
  
  
• Chain 'I':
  No sequence available.
  
  
• Chain 'J':
  No sequence available.
  
  
• Chain 'K':
  No sequence available.
  
  
• Chain 'L':
  No sequence available.
  
  
• Chain 'M':
  Sequence, based on SEQRES records: (download)
  

  >5kafM (M:)
  mevnqlgliatalfvlvpsvfliilyvqtesqqkss
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5kafM (M:)
  mevnqlgliatalfvlvpsvfliilyvqtesqq
  

  
  
• Chain 'O':
  No sequence available.
  
  
• Chain 'R':
  No sequence available.
  
  
• Chain 'T':
  No sequence available.
  
  
• Chain 'U':
  No sequence available.
  
  
• Chain 'V':
  No sequence available.
  
  
• Chain 'X':
  No sequence available.
  
  
• Chain 'Y':
  No sequence available.
  
  
• Chain 'Z':
  No sequence available.
  
  
• Chain 'a':
  No sequence available.
  
  
• Chain 'b':
  No sequence available.
  
  
• Chain 'c':
  No sequence available.
  
  
• Chain 'd':
  No sequence available.
  
  
• Chain 'e':
  No sequence available.
  
  
• Chain 'f':
  Sequence, based on SEQRES records: (download)
  

  >5kaff (f:)
  mtsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5kaff (f:)
  sypiftvrwvavhtlavptifflgaiaamqfiqr
  

  
  
• Chain 'h':
  No sequence available.
  
  
• Chain 'i':
  No sequence available.
  
  
• Chain 'j':
  No sequence available.
  
  
• Chain 'k':
  No sequence available.
  
  
• Chain 'l':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >5kafl (l:)
  mepnpnrqpvelnrtslylglllilvlallfssyffn
  

  
  
• Chain 'm':
  No sequence available.
  
  
• Chain 'o':
  Sequence, based on SEQRES records: (download)
  

  >5kafo (o:)
  mkyrilmatllavclgifslsapafaakqtltyddivgtglankcptlddtargaypids
  sqtyriarlclqpttflvkeepknkrqeaefvptklvtrettsldqiqgelkvnsdgslt
  fveedgidfqpvtvqmaggeripllftvknlvastqpnvtsittstdfkgefnvpsyrta
  nfldpkgrglasgydsaialpqakeeelaranvkrfsltkgqislnvakvdgrtgeiagt
  feseqlsdddmgahephevkiqgvfyasiepa
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5kafo (o:)
  qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
  aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
  knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
  aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
  iepa
  

  
  
• Chain 'r':
  No sequence available.
  
  
• Chain 't':
  No sequence available.
  
  
• Chain 'u':
  No sequence available.
  
  
• Chain 'v':
  No sequence available.
  
  
• Chain 'x':
  No sequence available.
  
  
• Chain 'y':
  No sequence available.
  
  
• Chain 'z':
  No sequence available.