PDBsum entry 5e7c

Photosynthesis

PDB id: 5e7c

Contents

Protein chains

334 a.a.

504 a.a.

451 a.a.

342 a.a.

81 a.a.

34 a.a.

65 a.a.

38 a.a.

38 a.a.

37 a.a.

37 a.a.

34 a.a.

243 a.a.

30 a.a.

97 a.a.

137 a.a.

29 a.a.

39 a.a.

62 a.a.

Ligands

OEX ×2

BCT ×2

CLA ×70

PHO ×4

BCR ×22

PL9 ×4

SQD ×8

LMG ×12

LHG ×10

DGD ×10

HEM

Metals

FE2

_CA ×6

_MG ×2

_CL ×6

PDB id:

5e7c

Name:

Photosynthesis

Title:

Macromolecular diffractive imaging using imperfect crystals - bragg data

Structure:

Photosystem ii protein d1 1. Chain: a, a. Synonym: psii d1 protein 1,photosystem ii q(b) protein 1. Other_details: photosystem 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:

4.50Å R-factor: 0.248 R-free: 0.275

Authors:

K.Ayyer,O.Yefanov,D.Oberthuer,S.Roy-Chowdhury,L.Galli,V.Mariani, S.Basu,J.Coe,C.E.Conrad,R.Fromme,A.Schaffner,K.Doerner,D.James, C.Kupitz,M.Metz,G.Nelson,P.L.Xavier,K.R.Beyerlein,M.Schmidt, I.Sarrou,J.C.H.Spence,U.Weierstall,T.A.White,J.-H.Yang,Y.Zhao, M.Liang,A.Aquila,M.S.Hunter,J.S.Robinson,J.E.Koglin,S.Boutet, P.Fromme,A.Barty,H.N.Chapman

Key ref:

K.Ayyer et al. (2016). Macromolecular diffractive imaging using imperfect crystals. Nature, 530, 202-206. PubMed id: 26863980 DOI: 10.1038/nature16949

Date:

12-Oct-15 Release date: 10-Feb-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: 342 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: 65 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: 38 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: 38 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: 34 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: 243 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: 29 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: 39 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.

* PDB and UniProt seqs differ at 1 residue position (black cross)

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/nature16949

Nature 530:202-206 (2016)

PubMed id: 26863980

Macromolecular diffractive imaging using imperfect crystals.

K.Ayyer, O.M.Yefanov, D.Oberthür, S.Roy-Chowdhury, L.Galli, V.Mariani, S.Basu, J.Coe, C.E.Conrad, R.Fromme, A.Schaffer, K.Dörner, D.James, C.Kupitz, M.Metz, G.Nelson, P.L.Xavier, K.R.Beyerlein, M.Schmidt, I.Sarrou, J.C.Spence, U.Weierstall, T.A.White, J.H.Yang, Y.Zhao, M.Liang, A.Aquila, M.S.Hunter, J.S.Robinson, J.E.Koglin, S.Boutet, P.Fromme, A.Barty, H.N.Chapman.

ABSTRACT

The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed--and are of interest as a source of information about the dynamics of proteins--they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.