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PDBsum entry 1yk5
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Electron transport
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PDB id
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1yk5
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References listed in PDB file
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Key reference
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Title
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Ultrahigh-Resolution study on pyrococcus abyssi rubredoxin. I. 0.69 a x-Ray structure of mutant w4l/r5s.
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Authors
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H.Bönisch,
C.L.Schmidt,
P.Bianco,
R.Ladenstein.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
990.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved
by direct methods. The model of the air-oxidized protein was refined by
partially restrained full-matrix least-squares refinement against intensity data
to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin
provides very detailed and precise information about the Fe(SCys)(4) centre and
its environment, the peptide-backbone stereochemistry, H atoms and hydrogen
bonds, static and dynamic disorder, the solvent structure and the
electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a
series of mutants studied by atomic and ultrahigh-resolution X-ray
crystallography which are expected to contribute to the understanding of
structure-function relationships in iron-sulfur proteins.
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Figure 3.
Figure 3
P. abyssi rubredoxin W4L/R5S. Electron-density maps calculated from the final model
refined to 0.69 Å resolution, superimposed onto the final model. (a) 2mF[o] - DF[c]
difference map of the redox centre; the contour level is 3.0 [sigma] . (b) 2mF[o] -
DF[c] difference map (white; contour level 3.0 [sigma] ) and proton-omit map (cyan;
contour level 2.0 [sigma] ) of the antiparallel [beta] -sheet. The main chain of
the final model is shown. D-H [\cdots] A and C-H [\cdots] O hydrogen bonds are
marked by red lines. (c) 2mF[o] - DF[c] difference map (white; contour level 3.0
[sigma] ) and proton omit map (cyan; contour level 2.0 [sigma] ) of a
hydrogen-bond network with well ordered solvent molecules. The hydrogen bonds are marked
by red lines. (d) 2mF[o] - DF[c] difference map (white; contour level 3.0 [sigma] )
and mF[o] - DF[c] difference map (green; contour level 2.0 [sigma] ) for residues
Asp14-Asp19 and Ser25-Thr28. The main chain of the final model is shown.
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Figure 4.
Figure 4
P. abyssi rubredoxin wild-type molecule A (cyan) and mutant W4L/R5S (atom colours).
Superposition of the Fe(SCys)[4] site.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
990-0)
copyright 2005.
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