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PDBsum entry 1gdv
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Electron transport
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PDB id
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1gdv
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of cytochrome c6 from the red alga porphyra yezoensis at 1. 57 a resolution.
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Authors
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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.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
1577-1582.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2000,
56,
1577-1582)
copyright 2000.
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