PDBsum entry 1gdv

Electron transport

PDB id: 1gdv

Contents

Protein chain

85 a.a. *

Ligands

HEC

Waters ×45

* Residue conservation analysis

PDB id:

1gdv

Name:

Electron transport

Title:

Crystal structure of cytochrome c6 from red alga porphyra yezoensis at 1.57 a resolution

Structure:

Cytochrome c6. Chain: a

Source:

Porphyra yezoensis. Organism_taxid: 2788

Resolution:

1.57Å R-factor: 0.199 R-free: 0.254

Authors:

S.Yamada,S.-Y.Park,H.Shimizu,Y.Shiro,T.Oku

Key ref:

S.Yamada et al. (2000). Structure of cytochrome c6 from the red alga Porphyra yezoensis at 1. 57 A resolution. Acta Crystallogr D Biol Crystallogr, 56, 1577-1582. PubMed id: 11092924 DOI: 10.1107/S090744490001461X

Date:

06-Oct-00 Release date: 06-Apr-01

Protein chain

Q8WKJ8  (CYC6_NEOYE) -  Cytochrome c6 from Neopyropia yezoensis

Seq: 110 a.a.

Struc: 85 a.a.

DOI no: 10.1107/S090744490001461X

Acta Crystallogr D Biol Crystallogr 56:1577-1582 (2000)

PubMed id: 11092924

Structure of cytochrome c6 from the red alga Porphyra yezoensis at 1. 57 A resolution.

S.Yamada, S.Y.Park, H.Shimizu, Y.Koshizuka, K.Kadokura, T.Satoh, K.Suruga, M.Ogawa, Y.Isogai, T.Nishio, Y.Shiro, T.Oku.

ABSTRACT

The crystal structure of cytochrome c(6) from the red alga Porphyra yezoensis has been determined at 1.57 A resolution. The crystal is tetragonal and belongs to space group P4(3)2(1)2, with unit-cell parameters a = b = 49.26 (3), c = 83.45 (4) A and one molecule per asymmetric unit. The structure was solved by the molecular-replacement method and refined with X-PLOR to an R factor of 19.9% and a free R factor of 25.4%. The overall structure of cytochrome c(6) follows the topology of class I c-type cytochromes in which the heme prosthetic group covalently binds to Cys14 and Cys17, and the iron has an octahedral coordination with His18 and Met58 as the axial ligands. The sequence and the structure of the eukaryotic red algal cytochrome c(6) are very similar to those of a prokaryotic cyanobacterial cytochrome c(6) rather than those of eukaryotic green algal c(6) cytochromes.

Selected figure(s)

Figure 2.
Figure 2 The overall structure of P. yezoensis cytochrome c[6]. The helices and -sheets (colored pink) are indicated as thick ribbons and the helices I-IV are numbered. The N- and C-termini are indicated. The heme prosthetic group and the heme-binding residues (Cys14, Cys17, His18 and Met58) are represented by ball-and-stick models in the same coloring scheme as Fig. 1-. The figure is drawn with the solvent-exposed heme edge at the front (the His iron ligand being on the right).

Figure 3.
Figure 3 The structure around the exposed heme edge of the cytochrome c[6]. The ribbon model shows the protein region (residues 14-59). The heme is represented in pink and the heme iron by a grey ball. Met26, Lys29, Met41, Gln50 and Lys55 are represented by ball-and-stick models in the same coloring scheme as Fig. 1-. Water molecules are represented as red balls. Possible hydrogen bonds are indicated by red dashed lines.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 1577-1582) copyright 2000.

Figures were selected by the author.