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PDBsum entry 1ar1
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Complex (oxidoreductase/antibody)
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PDB id
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1ar1
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Contents |
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529 a.a.
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252 a.a.
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118 a.a.
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108 a.a.
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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 at 2.7 a resolution of the paracoccus denitrificans two-Subunit cytochrome c oxidase complexed with an antibody fv fragment.
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Authors
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C.Ostermeier,
A.Harrenga,
U.Ermler,
H.Michel.
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Ref.
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Proc Natl Acad Sci U S A, 1997,
94,
10547-10553.
[DOI no: ]
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PubMed id
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Abstract
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The aa3 type cytochrome c oxidase consisting of the core subunits I and II only
was isolated from the soil bacterium Paracoccus denitrificans and crystallized
as complex with a monoclonal antibody Fv fragment. Crystals could be grown in
the presence of a number of different nonionic detergents. However, only
undecyl-beta-D-maltoside and cyclohexyl-hexyl-beta-D-maltoside yielded
well-ordered crystals suitable for high resolution x-ray crystallographic
studies. The crystals belong to space group P212121 and diffract x-rays to at
least 2.5 A (1 A = 0.1 nm) resolution using synchrotron radiation. The structure
was determined to a resolution of 2.7 A using molecular replacement and refined
to a crystallographic R-factor of 20.5% (Rfree = 25.9%). The refined model
includes subunits I and II and the 2 chains of the Fv fragment, 2 heme A
molecules, 3 copper atoms, and 1 Mg/Mn atom, a new metal (Ca) binding site, 52
tentatively identified water molecules, and 9 detergent molecules. Only four of
the water molecules are located in the cytoplasmic half of cytochrome c oxidase.
Most of them are near the interface of subunits I and II. Several waters form a
hydrogen-bonded cluster, including the heme propionates and the Mg/Mn binding
site. The Fv fragment binds to the periplasmic polar domain of subunit II and is
critically involved in the formation of the crystal lattice. The crystallization
procedure is well reproducible and will allow for the analysis of the structures
of mechanistically interesting mutant cytochrome c oxidases.
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Figure 1.
Fig. 1. Ribbon representation of the structure of the
two-subunit cytochrome c oxidase from P. denitrificans complexed
with the antibody F[v] fragment 7E2. Subunit I, olive green;
subunit II, dark red; F[v] fragment, blue; heme a, red; heme
a[3], blue; copper atoms, dark blue spheres; water molecules,
green spheres. The programs MOLSCRIPT (29) and RASTER 3D (30)
were used to prepare the figure.
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Figure 6.
Fig. 6. The hydrogen bonded network between the heme groups
and Cu[A]. Residues of subunit I are shown in olive green, those
of subunit II in dark red, copper atoms are dark blue spheres,
iron atoms dark red spheres, the Mg/Mn atom is a blue sphere,
water molecules are green spheres, heme a is red, and heme a[3]
is blue. The figure^ was produced using the programs MOLSCRIPT
(29) and RASTER 3D^ (30).
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