PDBsum entry 5kaf

Electron transport

PDB id: 5kaf

Contents

Protein chains

334 a.a.

504 a.a.

451 a.a.

341 a.a.

81 a.a.

34 a.a.

63 a.a.

36 a.a.

36 a.a.

37 a.a.

37 a.a.

33 a.a.

244 a.a.

30 a.a.

97 a.a.

137 a.a.

30 a.a.

38 a.a.

62 a.a.

34 a.a.

Ligands

OEX ×2

SQD ×9

CLA ×70

PHO ×4

BCR ×22

PL9 ×4

LMG ×16

UNL ×17

LHG ×10

BCT ×2

DGD

HEM ×2

HEC ×2

Metals

FE2

_CL

Waters ×124

PDB id:

5kaf

Name:

Electron transport

Title:

Rt xfel structure of photosystem ii in the dark state at 3.0 a resolution

Structure:

Photosystem ii protein d1 1. Chain: a, a. Fragment: unp residues 1-344. Synonym: psii d1 protein 1,photosystem ii q(b) protein 1. Photosystem ii cp47 reaction center protein. Chain: b, b. Synonym: psii 47 kda protein,protein cp-47. Photosystem ii cp43 reaction center protein. Chain: c, c.

Source:

Thermosynechococcus elongatus (strain bp-1). Organism_taxid: 197221. Strain: bp-1. Strain: bp-1

Resolution:

3.00Å R-factor: 0.264 R-free: 0.303

Authors:

I.D.Young,M.Ibrahim,R.Chatterjee,S.Gul,S.Koroidov,A.S.Brewster, R.Tran,R.Alonso-Mori,F.Fuller,T.Kroll,T.Michels-Clark,H.Laksmono, R.G.Sierra,C.A.Stan,C.Saracini,M.A.Bean,I.Seuffert,D.Sokaras,T.- C.Weng,M.S.Hunter,A.Aquila,J.E.Koglin,J.Robinson,M.Liang,S.Boutet, A.Y.Lyubimov,M.Uervirojnangkoorn,N.W.Moriarty,D.Liebschner, P.V.Afonine,D.G.Waterman,G.Evans,H.Dobbek,W.I.Weis,A.T.Brunger, P.H.Zwart,P.D.Adams,A.Zouni,J.Messinger,U.Bergmann,N.K.Sauter, J.Kern,V.K.Yachandra,J.Yano

Key ref:

I.D.Young et al. (2016). Structure of photosystem II and substrate binding at room temperature. Nature, 540, 453-457. PubMed id: 27871088 DOI: 10.1038/nature20161

Date:

01-Jun-16 Release date: 23-Nov-16

Protein chains

P0A444  (PSBA1_THEEB) -  Photosystem II protein D1 1 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 360 a.a.

Struc: 334 a.a.

Protein chains

Q8DIQ1  (PSBB_THEEB) -  Photosystem II CP47 reaction center protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 510 a.a.

Struc: 504 a.a.

Protein chains

Q8DIF8  (PSBC_THEEB) -  Photosystem II CP43 reaction center protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 461 a.a.

Struc: 451 a.a.

Protein chains

Q8CM25  (PSBD_THEEB) -  Photosystem II D2 protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 352 a.a.

Struc: 341 a.a.

Protein chains

Q8DIP0  (PSBE_THEEB) -  Cytochrome b559 subunit alpha from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 84 a.a.

Struc: 81 a.a.

Protein chains

Q8DIN9  (PSBF_THEEB) -  Cytochrome b559 subunit beta from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 45 a.a.

Struc: 34 a.a.

Protein chains

Q8DJ43  (PSBH_THEEB) -  Photosystem II reaction center protein H from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 66 a.a.

Struc: 63 a.a.

Protein chains

Q8DJZ6  (PSBI_THEEB) -  Photosystem II reaction center protein I from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 38 a.a.

Struc: 36 a.a.*

Protein chains

P59087  (PSBJ_THEEB) -  Photosystem II reaction center protein J from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 40 a.a.

Struc: 36 a.a.

Protein chains

Q9F1K9  (PSBK_THEEB) -  Photosystem II reaction center protein K from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 46 a.a.

Struc: 37 a.a.

Protein chains

Q8DIN8  (PSBL_THEEB) -  Photosystem II reaction center protein L from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 37 a.a.

Struc: 37 a.a.

Protein chains

Q8DHA7  (PSBM_THEEB) -  Photosystem II reaction center protein M from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 36 a.a.

Struc: 33 a.a.*

Protein chains

P0A431  (PSBO_THEEB) -  Photosystem II extrinsic protein O from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 272 a.a.

Struc: 244 a.a.

Protein chains

Q8DIQ0  (PSBT_THEEB) -  Photosystem II reaction center protein T from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 32 a.a.

Struc: 30 a.a.*

Protein chains

Q9F1L5  (PSBU_THEEB) -  Photosystem II extrinsic protein U from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 134 a.a.

Struc: 97 a.a.

Protein chains

P0A386  (CY550_THEEB) -  Photosystem II extrinsic protein V from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 163 a.a.

Struc: 137 a.a.

Protein chains

Q8DJI1  (YCF12_THEEB) -  Photosystem II reaction center protein Psb30 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 46 a.a.

Struc: 30 a.a.

Protein chains

Q9F1R6  (PSBX_THEEB) -  Photosystem II reaction center protein X from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 41 a.a.

Struc: 38 a.a.

Protein chains

Q8DHJ2  (PSBZ_THEEB) -  Photosystem II reaction center protein Z from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 62 a.a.

Struc: 62 a.a.

Protein chains

Q8DKM3  (PSBY_THEEB) -  Photosystem II reaction center protein Y from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 41 a.a.

Struc: 34 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, D, a, d: E.C.1.10.3.9 - photosystem Ii.
• Reaction: 2 a plastoquinone + 4 hnu + 2 H2O = 2 a plastoquinol + O2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1038/nature20161

Nature 540:453-457 (2016)

PubMed id: 27871088

Structure of photosystem II and substrate binding at room temperature.

I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.de Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Bräuer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano.

ABSTRACT

No abstract given.