4YUU

Crystal structure of oxygen-evolving photosystem II from a red alga


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga

Ago, H.Adachi, H.Umena, Y.Tashiro, T.Kawakami, K.Kamiya, N.Tian, L.Han, G.Kuang, T.Liu, Z.Wang, F.Zou, H.Enami, I.Miyano, M.Shen, J.-R.

(2016) J Biol Chem 291: 5676-5687

  • DOI: 10.1074/jbc.M115.711689
  • Primary Citation of Related Structures:  
    4YUU

  • PubMed Abstract: 
  • Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed ...

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.


    Related Citations: 
    • Towards structural elucidation of eukaryotic photosystem II: Purification, crystallization and preliminary X-ray diffraction analysis of photosystem II from a red alga.
      Adachi, H., Umena, Y., Enami, I., Henmi, T., Kamiya, N., Shen, J.-R.
      (2009) Biochim Biophys Acta 1787: 121

    Organizational Affiliation

    the Photosynthesis Research Center, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan, the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China, shen@cc.okayama-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1A [auth A1], PA [auth A2], U [auth a1], LB [auth a2]344Cyanidium caldariumMutation(s): 0 
Gene Names: psbA
EC: 1.10.3.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19895 (Cyanidium caldarium)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB [auth B1], QA [auth B2], V [auth b1], MB [auth b2]509Cyanidium caldariumMutation(s): 0 
Gene Names: psbB
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19928 (Cyanidium caldarium)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC [auth C1], RA [auth C2], W [auth c1], NB [auth c2]460Cyanidium caldariumMutation(s): 0 
Gene Names: psbC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM46 (Cyanidium caldarium)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD [auth D1], SA [auth D2], X [auth d1], OB [auth d2]351Cyanidium caldariumMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM47 (Cyanidium caldarium)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE [auth E1], TA [auth E2], Y [auth e1], PB [auth e2]84Cyanidium caldariumMutation(s): 0 
Gene Names: psbE
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM20 (Cyanidium caldarium)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF [auth F1], UA [auth F2], Z [auth f1], QB [auth f2]43Cyanidium caldariumMutation(s): 0 
Gene Names: psbF
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM21 (Cyanidium caldarium)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H1], VA [auth H2], AA [auth h1], RB [auth h2]67Cyanidium caldariumMutation(s): 0 
Gene Names: psbH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19925 (Cyanidium caldarium)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I1], WA [auth I2], BA [auth i1], SB [auth i2]38Cyanidium caldariumMutation(s): 0 
Gene Names: psbI
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19882 (Cyanidium caldarium)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J1], XA [auth J2], CA [auth j1], TB [auth j2]39Cyanidium caldariumMutation(s): 0 
Gene Names: psbJ
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM23 (Cyanidium caldarium)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K1], YA [auth K2], DA [auth k1], UB [auth k2]41Cyanidium caldariumMutation(s): 0 
Gene Names: psbK
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TLR0 (Cyanidium caldarium)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L1], ZA [auth L2], EA [auth l1], VB [auth l2]38Cyanidium caldariumMutation(s): 0 
Gene Names: psbL
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM22 (Cyanidium caldarium)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM II REACTION CENTER PROTEIN ML [auth M1], AB [auth M2], FA [auth m1], WB [auth m2]108Cyanidium caldariumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBOM [auth O1], BB [auth O2], GA [auth o1], XB [auth o2]329Cyanidium caldariumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T1], CB [auth T2], HA [auth t1], YB [auth t2]32Cyanidium caldariumMutation(s): 0 
Gene Names: psbT
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19927 (Cyanidium caldarium)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic protein, chloroplasticO [auth U1], DB [auth U2], IA [auth u1], ZB [auth u2]155Cyanidium caldariumMutation(s): 0 
Gene Names: psbU
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9ZQS5 (Cyanidium caldarium)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V1], EB [auth V2], JA [auth v1], AC [auth v2]155Cyanidium caldariumMutation(s): 0 
Gene Names: psbV
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q76FB0 (Cyanidium caldarium)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12Q [auth Y1], FB [auth Y2], KA [auth y1], BC [auth y2]35Cyanidium caldariumMutation(s): 0 
Gene Names: ycf12ycf34
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TLX0 (Cyanidium caldarium)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM II REACTION CENTER PROTEIN XR [auth X1], GB [auth X2], LA [auth x1], CC [auth x2]40Cyanidium caldariumMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE CHAIN UNASSIGNEDS [auth S1], HB [auth S2], MA [auth s1], DC [auth s2]46Cyanidium caldariumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE CHAIN UNASSIGNEDT [auth W1], IB [auth W2], NA [auth w1], EC [auth w2]25Cyanidium caldariumMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIJB [auth Q2], OA [auth q1]218Cyanidium caldariumMutation(s): 0 
Gene Names: psbQ'
Find proteins for Q76B86 (Cyanidium caldarium)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZKB [auth Z2], FC [auth z2]62Cyanidium caldariumMutation(s): 0 
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Small Molecules
Ligands 17 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DP [auth h2] , HE [auth C1] , IE [auth C1] , JE [auth C1] , JO [auth c2] , KI [auth h1] , LO [auth c2] , MO [auth c2] , 
DP [auth h2],  HE [auth C1],  IE [auth C1],  JE [auth C1],  JO [auth c2],  KI [auth h1],  LO [auth c2],  MO [auth c2],  QH [auth c1],  QL [auth H2],  UH [auth c1],  WH [auth c1],  XK [auth C2],  ZE [auth H1]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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AD [auth B1] , AE [auth C1] , AJ [auth A2] , AK [auth B2] , AN [auth b2] , AO [auth c2] , BD [auth B1] , BE [auth C1] , 
AD [auth B1],  AE [auth C1],  AJ [auth A2],  AK [auth B2],  AN [auth b2],  AO [auth c2],  BD [auth B1],  BE [auth C1],  BG [auth b1],  BI [auth d1],  BJ [auth A2],  BK [auth B2],  BL [auth C2],  BO [auth c2],  CD [auth B1],  CE [auth C1],  CG [auth b1],  CK [auth B2],  CN [auth b2],  CO [auth c2],  DD [auth B1],  DE [auth C1],  DG [auth b1],  DI [auth d1],  DK [auth B2],  DL [auth C2],  DO [auth c2],  ED [auth B1],  EE [auth C1],  EG [auth b1],  EL [auth D2],  EN [auth b2],  EO [auth c2],  FD [auth B1],  FE [auth C1],  FG [auth b1],  FH [auth c1],  FN [auth b2],  FO [auth c2],  GD [auth B1],  GE [auth C1],  GG [auth b1],  GH [auth c1],  GN [auth b2],  GO [auth c2],  HD [auth B1],  HG [auth b1],  HH [auth c1],  HL [auth D2],  HN [auth b2],  HO [auth c2],  IC [auth A1],  ID [auth B1],  IG [auth b1],  IH [auth c1],  IN [auth b2],  IO [auth c2],  JC [auth A1],  JD [auth B1],  JG [auth b1],  JH [auth c1],  JL [auth D2],  JM [auth a2],  JN [auth b2],  KC [auth A1],  KD [auth B1],  KG [auth b1],  KH [auth c1],  KM [auth a2],  KN [auth b2],  KO [auth c2],  LC [auth A1],  LD [auth B1],  LG [auth b1],  LH [auth c1],  LN [auth b2],  MG [auth b1],  MH [auth c1],  MN [auth b2],  NF [auth a1],  NG [auth b1],  NH [auth c1],  NN [auth b2],  OF [auth a1],  OG [auth b1],  OH [auth c1],  OJ [auth B2],  OK [auth C2],  ON [auth b2],  PE [auth D1],  PF [auth a1],  PH [auth c1],  PJ [auth B2],  PK [auth C2],  PN [auth b2],  QE [auth D1],  QG [auth b1],  QJ [auth B2],  QK [auth C2],  QN [auth b2],  RG [auth b1],  RH [auth c1],  RJ [auth B2],  RK [auth C2],  RO [auth d2],  SH [auth c1],  SJ [auth B2],  SK [auth C2],  SM [auth a2],  TJ [auth B2],  TK [auth C2],  TO [auth d2],  UD [auth C1],  UJ [auth B2],  UK [auth C2],  UN [auth b2],  UO [auth d2],  VD [auth C1],  VJ [auth B2],  VK [auth C2],  WC [auth B1],  WD [auth C1],  WJ [auth B2],  WK [auth C2],  XC [auth B1],  XD [auth C1],  XJ [auth B2],  XL [auth K2],  XN [auth c2],  YC [auth B1],  YD [auth C1],  YH [auth d1],  YJ [auth B2],  YK [auth C2],  YN [auth c2],  ZC [auth B1],  ZD [auth C1],  ZI [auth A2],  ZJ [auth B2],  ZN [auth c2]
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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AI [auth d1], EJ [auth A2], KL [auth D2], NC [auth A1], UE [auth D1], VF [auth a1], VM [auth a2], XO [auth d2]PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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BN [auth b2], FL [auth D2], HK [auth B2], WE [auth D1]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LMG
Query on LMG

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AL [auth C2] , CH [auth b1] , EK [auth B2] , FF [auth M1] , FI [auth d1] , FK [auth B2] , GP [auth j2] , II [auth d1] , 
AL [auth C2],  CH [auth b1],  EK [auth B2],  FF [auth M1],  FI [auth d1],  FK [auth B2],  GP [auth j2],  II [auth d1],  JJ [auth A2],  ME [auth C1],  OD [auth B1],  OL [auth F2],  OO [auth c2],  PC [auth A1],  RC [auth A1],  RM [auth a2],  SD [auth B1],  SG [auth b1],  SN [auth b2],  TE [auth D1],  TL [auth I2],  VG [auth b1],  VH [auth c1],  WF [auth a1],  WO [auth d2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

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GI [auth d1], LL [auth D2], VE [auth D1], YO [auth d2]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
LHG
Query on LHG

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BM [auth L2] , CJ [auth A2] , DF [auth L1] , EI [auth d1] , GL [auth D2] , IL [auth D2] , LK [auth B2] , MM [auth a2] , 
BM [auth L2],  CJ [auth A2],  DF [auth L1],  EI [auth d1],  GL [auth D2],  IL [auth D2],  LK [auth B2],  MM [auth a2],  ND [auth B1],  NP [auth l2],  QI [auth l1],  RE [auth D1],  RF [auth a1],  SE [auth D1],  SO [auth d2],  TG [auth b1],  VN [auth b2],  VO [auth d2],  ZH [auth d1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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BP [auth e2], DM [auth V2], JI [auth f1], KF [auth V1], ML [auth E2], TP [auth v2], WI [auth v1], YE [auth E1]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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AF [auth H1] , AG [auth b1] , AM [auth K2] , BF [auth J1] , CF [auth K1] , CI [auth d1] , CP [auth h2] , DH [auth c1] , 
AF [auth H1],  AG [auth b1],  AM [auth K2],  BF [auth J1],  CF [auth K1],  CI [auth d1],  CP [auth h2],  DH [auth c1],  EH [auth c1],  GC [auth A1],  HM [auth a2],  HP [auth j2],  IP [auth k2],  LF [auth a1],  LI [auth h1],  LJ [auth B2],  MJ [auth B2],  NE [auth C1],  NJ [auth B2],  NK [auth C2],  NL [auth F2],  OE [auth D1],  OI [auth k1],  QO [auth d2],  SL [auth H2],  TC [auth B1],  TD [auth C1],  UC [auth B1],  UP [auth z2],  VC [auth B1],  WN [auth c2],  XM [auth b2],  YF [auth b1],  YI [auth A2],  YL [auth K2],  YM [auth b2],  ZF [auth b1],  ZM [auth b2]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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EF [auth L1] , FP [auth i2] , GF [auth M1] , HF [auth M1] , JF [auth T1] , LE [auth C1] , LM [auth a2] , PI [auth l1] , 
EF [auth L1],  FP [auth i2],  GF [auth M1],  HF [auth M1],  JF [auth T1],  LE [auth C1],  LM [auth a2],  PI [auth l1],  QP [auth m2],  RN [auth b2],  RP [auth m2],  SI [auth m1],  TH [auth c1],  TN [auth b2]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX
Query on OEX

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DJ [auth A2], MC [auth A1], NM [auth a2], SF [auth a1]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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KE [auth C1] , MD [auth B1] , MI [auth i1] , NO [auth c2] , PG [auth b1] , QF [auth a1] , UM [auth a2] , XH [auth c1] , 
KE [auth C1],  MD [auth B1],  MI [auth i1],  NO [auth c2],  PG [auth b1],  QF [auth a1],  UM [auth a2],  XH [auth c1],  ZK [auth C2]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
KJ [auth A2], SC [auth A1], WM [auth a2], XF [auth a1]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
IJ [auth A2], QC [auth A1], TM [auth a2], UF [auth a1]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
IF [auth O1], SP [auth o2]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
HC [auth A1], HJ [auth A2], IM [auth a2], MF [auth a1]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AH [auth b1] , AP [auth d2] , BH [auth b1] , CL [auth C2] , CM [auth M2] , DN [auth b2] , EM [auth X2] , EP [auth i2] , 
AH [auth b1],  AP [auth d2],  BH [auth b1],  CL [auth C2],  CM [auth M2],  DN [auth b2],  EM [auth X2],  EP [auth i2],  FJ [auth A2],  FM [auth W2],  GJ [auth A2],  GK [auth B2],  GM [auth a2],  HI [auth d1],  IK [auth B2],  JK [auth B2],  JP [auth k2],  KK [auth B2],  KP [auth k2],  LP [auth k2],  MK [auth C2],  MP [auth k2],  NI [auth j1],  OC [auth A1],  OM [auth a2],  OP [auth m2],  PD [auth B1],  PL [auth F2],  PM [auth a2],  PO [auth c2],  PP [auth m2],  QD [auth B1],  QM [auth a2],  RD [auth B1],  RI [auth l1],  RL [auth H2],  TF [auth a1],  TI [auth m1],  UG [auth b1],  UI [auth t1],  UL [auth I2],  VI [auth t1],  VL [auth I2],  WG [auth b1],  WL [auth J2],  XE [auth D1],  XG [auth b1],  XI [auth x1],  YG [auth b1],  ZG [auth b1],  ZL [auth K2],  ZO [auth d2]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.445α = 90
b = 240.31β = 90
c = 300.063γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-19 
  • Released Date: 2016-01-20 
  • Deposition Author(s): Ago, H., Shen, J.-R.

Funding OrganizationLocationGrant Number
JSPSJapan24000018

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations