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Atomic coordinates for ferricytochrome c2 of Rhodospirillum rubrum
BIOCHEMICAL
Vol. 54, No. 1,1973
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
ATOMICCOORDINATES FORFERRICYTOCHROME 22 OF RHODOSPIRILLUM RUBRUM F. R. Salemme,S. T. Freer, R. A. Alden and J. Kraut Department of Chemistry University of California, San Diego La Jolla, California 92037 Received
July
12,
1973
Summary: Atomic coordinates and backbone torsion angles are tabulated for ferricytochrome c2 of Rhodospirillum rubrum. The three-dimensional thetic
structure
c,2 of the photosyn-
bacterium Rhodospirillum rubrum has been described in a previous
publication
(1).
This protein,
donor to bacteriochlorophyll transport tial
of ferricytochrome
of MW= 12,480, functions
in the cyclic
photophosphorylating
chain of the bacterium, and is of interest
and structural
similarity
as the electron
with eucaryotic
electron
because of its sequen-
mitochondrial
cytochrome c
(2-4). Cytochrome z2 is composedof a single polypeptide chain of 112 amino acid residues and contains a single protoheme IX covalently polypeptide
chain through thioether
linkages formed between the heme vinyl
side chains and cysteine residues 14 and 17. to the Ns2 nitrogen atom of histidine 91 in the fifth
bonded to the
and sixth positions,
The hemeiron is coordinated
18 and the S6 sulfur respectively.
atom
The hemegroup is planar,
as expected for a low-spin ferriheme coordinate complex (5). atom of methionine 91 appears, however, to be slightly 0.3 x) from its expected axial (ref.
The S6 sulfur
displaced (about
position in a regular octahedral iron complex
1, Fig. 5). Coordinates of cytochrome c2 were initially
measuredby meansof an
automated coordinate measuring device (6) on a model built optical
in a Richards
comparator (7) from a 2 % multiple-isomorphous-replacement
map. These initial will
of methionine
phased
coordinates were subsequently refined by techniques which
be described in detail
Copyright 0 1973 by Academic Press, Inc. All rights of reproduction in any form reserved.
in a communication currently 47
in preparation
(8).
BIOCHEMICAL
Vol. 54, No. 1, 1973
AND BIOPHYSICAL
Table
RESEARCH COMMUNICATIONS
I:
f”8
PWE
“9 OG “9 c
48
BIOCHEMICAL
Vol. 54, No. 1, 1973
Table
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
I (continued)
I”.” I”.” 13.1 13.” 12.7 12.7 11.7 10.3
LL”
:: ::: ::: 5.2 2: u.3 3.5 5.3 5.6 7.1 :*,’ 9:* ::: 3.” 2: 3.3 2.9 1.6 2: 1.1
13.” 11.1 11.1 11.8 12.7 13.3 13.5 II.5 11.9
l,.” 11.9 11.3 1,‘:: 2: 9.8 11.1 11.7 10.2 10.0 2:
49
1::: 12.” 12.5 12.1 (1.8 10.11 9.8 8.3 7.8 6.3 11.9 12.2 11.6 l,., 10.7 11.5 9.” 13.1 13.7 13.8 15.2 15.5 15.1 14.6 14.6 15.9 16-i (6.1 16.8 16.0 11.5 18.0 18.C 16.6 16.8 16.8 (6.9
17.9 16.9 16.9 17.” 17.7 18.1 17.2 19.” 19.8 19.3 30.0 20.0 19. 3 19.” 21.3 21.6 22.1 23.1 2u.2 21.0 23.3 23.9 2Y.7 23.” 23.7 23.5 2U.B 25.9 2u.u 22.6 21.5 23.0 **., 20.8 19.7 19.3 18.” 18.0 22.9 21.1 22.1
Vol. 54, No. 1, 1973
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Table
I
Table
The coordinates listed tallographic
II
here derive from an intermediate
refinement including all
120 water molecules (not listed). fitted
(continued)
stage of the crys-
904 atoms of the protein molecule plus
These coordinates (Table I) have been
to standard groups by a version of R. Diamond's model building
gram (9), and yield a structure R=
with a crystallographic
pro-
R factor
cl IFol-IF,1 I = 44 5% .
o-,I The coordinates in Table I are given in xngstrom units in a righthanded Cartesian system for convenience in model building. verted to orthorhombic fractional following
crystallographic
They may be con-
coordinates by the
transformation: Xtryst
= (310X + 6214)10-4
Ytryst Z tryst
= (2681 + 4781)10-4 = (1182 t 1972)10-4
where X, Y, and Z are the Cartesian coordinates given in Table I. 22 crystallized
Cytochrome
in space group P212121 with a = 32.3, b = 37.4, and c = 04.6 i.
Table II gives the interpeptide
dihedral angles, $ and $, according to
50
Vol. 54, No. 1, 1973
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
‘\ SG Cyrl7)
4
30
381
3cc
302
Fig.
1.
Fig.
2.
51
Vol. 54, No. 1, 1973
BIOCHEMICAL
the IUPAC-IUB convention (10).
AND BIOPHYSKAL
RESEARCH COMMUNICATIONS
Fig. 1 shows the convention for labeling
atoms of the protoheme IX ring.
Fig, 2 is a stereo drawing of the z2 mole-
cule showing a-carbon positions,
hemeligands,
and aromatic residues.
This work was supported by research grants from the National Institutes of Health (GM 10928, GM16717) and the National Science Foundation (GB 15684, GB 23054, GB 30828X) and by Public Health Service Research Career Development Awards to S.T.F.
and R.A.A. from the National Institute
of General Medical
Sciences (GM 70-140, GM 15401). REFERENCES 1. 2. 3. 4. 5. 6. 7. 8. 9.
10.
Salemme, F. R., Freer, S. T., Alden, R. A., Xuong, Ng. H., and Kraut, J. (1973) J. Biol. Chem. 248, 3910. Dickerson, R. E. (1972nci. Amer. 226, No. 4, 58-67. Timkovich, R., and Dickerson, R. E.T973) J. Biol. Chem., in press. Salemme, F. R., Kraut, J., and Kamen, M. D. (1973) J. Biol. Chem., submitted for publication. Countryman, R., Collins, D. M., and Hoard, J. L. (1969) J. Am. Chem. Sot. 2, 5166-5167. Salemme, F. R., and Fehr, D. G. (1972) J. Mol. Biol. 2, 697-700. Richards, F. M. (1968) J. Mol. Biol. 37, 225-229, Freer, S. T., Alden, R. A., Salemme, F. R., and Kraut, J. (1973) in preparation. Diamond, R. (1966) Acta Cryst. 21, 253-259. IUPAC-IUB Commissionon Biochemzal Nomenclature (1970) Biochemistry 2, 3471-3475.
52
Vol. 54, No. 1,1973
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
ATOMICCOORDINATES FORFERRICYTOCHROME 22 OF RHODOSPIRILLUM RUBRUM F. R. Salemme,S. T. Freer, R. A. Alden and J. Kraut Department of Chemistry University of California, San Diego La Jolla, California 92037 Received
July
12,
1973
Summary: Atomic coordinates and backbone torsion angles are tabulated for ferricytochrome c2 of Rhodospirillum rubrum. The three-dimensional thetic
structure
c,2 of the photosyn-
bacterium Rhodospirillum rubrum has been described in a previous
publication
(1).
This protein,
donor to bacteriochlorophyll transport tial
of ferricytochrome
of MW= 12,480, functions
in the cyclic
photophosphorylating
chain of the bacterium, and is of interest
and structural
similarity
as the electron
with eucaryotic
electron
because of its sequen-
mitochondrial
cytochrome c
(2-4). Cytochrome z2 is composedof a single polypeptide chain of 112 amino acid residues and contains a single protoheme IX covalently polypeptide
chain through thioether
linkages formed between the heme vinyl
side chains and cysteine residues 14 and 17. to the Ns2 nitrogen atom of histidine 91 in the fifth
bonded to the
and sixth positions,
The hemeiron is coordinated
18 and the S6 sulfur respectively.
atom
The hemegroup is planar,
as expected for a low-spin ferriheme coordinate complex (5). atom of methionine 91 appears, however, to be slightly 0.3 x) from its expected axial (ref.
The S6 sulfur
displaced (about
position in a regular octahedral iron complex
1, Fig. 5). Coordinates of cytochrome c2 were initially
measuredby meansof an
automated coordinate measuring device (6) on a model built optical
in a Richards
comparator (7) from a 2 % multiple-isomorphous-replacement
map. These initial will
of methionine
phased
coordinates were subsequently refined by techniques which
be described in detail
Copyright 0 1973 by Academic Press, Inc. All rights of reproduction in any form reserved.
in a communication currently 47
in preparation
(8).
BIOCHEMICAL
Vol. 54, No. 1, 1973
AND BIOPHYSICAL
Table
RESEARCH COMMUNICATIONS
I:
f”8
PWE
“9 OG “9 c
48
BIOCHEMICAL
Vol. 54, No. 1, 1973
Table
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
I (continued)
I”.” I”.” 13.1 13.” 12.7 12.7 11.7 10.3
LL”
:: ::: ::: 5.2 2: u.3 3.5 5.3 5.6 7.1 :*,’ 9:* ::: 3.” 2: 3.3 2.9 1.6 2: 1.1
13.” 11.1 11.1 11.8 12.7 13.3 13.5 II.5 11.9
l,.” 11.9 11.3 1,‘:: 2: 9.8 11.1 11.7 10.2 10.0 2:
49
1::: 12.” 12.5 12.1 (1.8 10.11 9.8 8.3 7.8 6.3 11.9 12.2 11.6 l,., 10.7 11.5 9.” 13.1 13.7 13.8 15.2 15.5 15.1 14.6 14.6 15.9 16-i (6.1 16.8 16.0 11.5 18.0 18.C 16.6 16.8 16.8 (6.9
17.9 16.9 16.9 17.” 17.7 18.1 17.2 19.” 19.8 19.3 30.0 20.0 19. 3 19.” 21.3 21.6 22.1 23.1 2u.2 21.0 23.3 23.9 2Y.7 23.” 23.7 23.5 2U.B 25.9 2u.u 22.6 21.5 23.0 **., 20.8 19.7 19.3 18.” 18.0 22.9 21.1 22.1
Vol. 54, No. 1, 1973
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Table
I
Table
The coordinates listed tallographic
II
here derive from an intermediate
refinement including all
120 water molecules (not listed). fitted
(continued)
stage of the crys-
904 atoms of the protein molecule plus
These coordinates (Table I) have been
to standard groups by a version of R. Diamond's model building
gram (9), and yield a structure R=
with a crystallographic
pro-
R factor
cl IFol-IF,1 I = 44 5% .
o-,I The coordinates in Table I are given in xngstrom units in a righthanded Cartesian system for convenience in model building. verted to orthorhombic fractional following
crystallographic
They may be con-
coordinates by the
transformation: Xtryst
= (310X + 6214)10-4
Ytryst Z tryst
= (2681 + 4781)10-4 = (1182 t 1972)10-4
where X, Y, and Z are the Cartesian coordinates given in Table I. 22 crystallized
Cytochrome
in space group P212121 with a = 32.3, b = 37.4, and c = 04.6 i.
Table II gives the interpeptide
dihedral angles, $ and $, according to
50
Vol. 54, No. 1, 1973
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
‘\ SG Cyrl7)
4
30
381
3cc
302
Fig.
1.
Fig.
2.
51
Vol. 54, No. 1, 1973
BIOCHEMICAL
the IUPAC-IUB convention (10).
AND BIOPHYSKAL
RESEARCH COMMUNICATIONS
Fig. 1 shows the convention for labeling
atoms of the protoheme IX ring.
Fig, 2 is a stereo drawing of the z2 mole-
cule showing a-carbon positions,
hemeligands,
and aromatic residues.
This work was supported by research grants from the National Institutes of Health (GM 10928, GM16717) and the National Science Foundation (GB 15684, GB 23054, GB 30828X) and by Public Health Service Research Career Development Awards to S.T.F.
and R.A.A. from the National Institute
of General Medical
Sciences (GM 70-140, GM 15401). REFERENCES 1. 2. 3. 4. 5. 6. 7. 8. 9.
10.
Salemme, F. R., Freer, S. T., Alden, R. A., Xuong, Ng. H., and Kraut, J. (1973) J. Biol. Chem. 248, 3910. Dickerson, R. E. (1972nci. Amer. 226, No. 4, 58-67. Timkovich, R., and Dickerson, R. E.T973) J. Biol. Chem., in press. Salemme, F. R., Kraut, J., and Kamen, M. D. (1973) J. Biol. Chem., submitted for publication. Countryman, R., Collins, D. M., and Hoard, J. L. (1969) J. Am. Chem. Sot. 2, 5166-5167. Salemme, F. R., and Fehr, D. G. (1972) J. Mol. Biol. 2, 697-700. Richards, F. M. (1968) J. Mol. Biol. 37, 225-229, Freer, S. T., Alden, R. A., Salemme, F. R., and Kraut, J. (1973) in preparation. Diamond, R. (1966) Acta Cryst. 21, 253-259. IUPAC-IUB Commissionon Biochemzal Nomenclature (1970) Biochemistry 2, 3471-3475.
52