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Atomic coordinates for tosyl-elastase
Vol. 53, No. 3,1973
BIOCHEMICAL
ATOMIC
Molecular Medical
Received
D.M.
Enzymology
Laboratory,
School,
accurate
Department
of Biochemistry,
Bristol,
set of non-hydrogen, given. This includes
2, 3).
BS8 lTD,
England.
model
atomic coordinates of porcine the tosyl group and the internal
pancreatic
elastase
Recently,
determination
atomic
Watson*
1973
(1,
structure
and H.C.
Walk,
of porcine
resolution
RESEARCH COMMUNICATIONS
FOR TOSYL-ELASTASE
Shotto
University
June 1,
The structure
the
COORDINATES
L. Sawyer,
Summary: The full tosyl elastase is water molecules.
3.52
AND BIOPHYSICAL
we have
extended
of tosyl-elastase
of the enzyme,
has been
to 2.52
the
coordinates
the
determined
at
resolution
of
and have built of which
are
an reported
here. High
resolution
derivatives new data
uously
as were were
reflexions
X-ray
positions
of the membered obvious. +
*
Present
To
density
of almost
representing
the
Sulphur
appears
clearly
side
and forking atoms
address:
chains
Copyrikht @ 1973 by Academic &-es, AN rights of reproduction in any form
Jnc. reserved.
of merit
from
being
these
0.86
in a clear
same
for
protrusions
clear,
with
side-chains
of Botany, California
are
the
Dimpling is, just
for
the Density exception
of sixthe most part,
resolved
University of California, 94720, U.S.A.
be addressed.
944
atoms.
residues.
bridges
indicating
oxygen
all
and unambig-
the map as a continuous
is also
polar
of disulphide
should
obtained
resulted
carbonyl
of branched
Department Berkeley,
whom correspondence
in
defined
of some surface
of the
map.
of the peptide
amino-acid
The phases
and this
density
chain
with all
extremities rings
and 2.51,
main
from crystals,
the mean figure
electron
The polypeptide of high
collected (2).
accuracy,
3.64x
interpretable
ribbon
were
used previously
of high
between
data
and
Vol. 53, No. 3,1973
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
.OlSr
0a c
65
95 Dlstonce -re
at twice
the main-chain
can be identified determined Asn-186
from
primary is very
the density
associated
tosyl
attached
group
sulphate
ion
are also
well
Using
alone,
is known
to deamidation
with
five
as a function of indicate the points
internal
confirming
indeed,
an aspartic
peaks centre
of the
from the
and,
with
protein,
to the active twenty
the
sequence
chemically work
the electron acid.
representing serine
residues
residue,
and many surface
that density
In addition
the positions
to of the
a surface-bound water
molecules,
(6,7),
a model
defined.
an optical
comparator
with
a vertical
from Kendrew-Watson
Engineers,
the electron
It
is more consistent
(4),
constructed
Repetition
of all
5
in cm
The majority
density
(5).
susceptible
point
density.
the electron
structure
map at that
been
35 mlrrcw
The mean error in the x-coordinate plotted the distance from the mirror. Error bars averaged over less than 100 observations.
I
appear
from
density
non-hydrogen
Greens
Road,
skeletal Cambridge,
map of tosyl-elastase. atoms
including
those
TABLE l(see
mirror components
has
(Cambridge
England)
which
fits
accurately
From this
model,
the coordinates
of the tosyl
group,
sulphate
ion
and
pp. 946-951) The measured coordinates are recorded in gngstrom units (O.lnm) measured from the origin of the unit cell (P2I2 2 ), along the crystallographic axes. Amino-acid residues are identified by 1 heir l. number in the chymotrypsinogen-A numbering scheme (5) to facilitate comparison. Atoms are identified according to the IUPAC-IUB conventions, 1970 (9) using Latin equivalents of Greek characters. ll has been transliterated as EH rather than H. The positions of the amino group and oxygen atom of amide side-chains have been determined from stereochemical considerations. An asterisk preceding an atomic coordinate indicates that that atom is not clearly visible in the electron rotating surface residues and density map. Such atoms belong to freely were built fully staggered.
945
Vol. 53, No. 3,1973
BIOCHEMICAL
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Vol. 53, No. 3, 1973
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Vol. 53, No. 3, 1973
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
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Vol. 53, No. 3, 1973
BlOCHEMlCAt
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
52.6
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Vol. 53, No. 3, 1973
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
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BIOCHEMICAL
Vol. 53, No. 3, 1973
HAT
16
MIT
-1.9
OH2
20.2
45.6
YLT 17 OH2 Y4T
29.3
-9.b
19
OH2 IdAT 20
-9.6
OH2 21
-9.2
on2
-9.9
56.1 WIT
18
on2
-?.I
internal
28.5
54.7
waters
described Gross
clerical
the output between
errors from
perpendicular
was 0.1881.
18.8
description
5.1
Y41
OH2 23 on2 21
4.4
35.1
30.2
U4f
on2
2.2
Sb.8
38.b
51.1
using
WIT
have
(10).
and those
obtained
of depth
produces as is
and its
57.8
31.1
so4
-8.5
21.8
68.9
of the device as measured.
been eliminated
using
deviation
by the model-building in the direction
variation
shown in Figure
of the structure
9.2
1
coordinates
The r.m.s.
perception
a systematic
25
on2
version the
programme
The problem
41.2 SUL
1 lists
measurement
coordinates
36.1
a simplified
Table
(8).
measurement
22
48.3
in coordinate
to the mirror
of the x-coordinate A full
and Fehr
MIT
46.4
19.6
a model-building
the measured
programme
18.6
have been measured
by Salemmi
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
in
the accuracy
I.
determination
is
in
preparation to us the We are grateful to Professor H. Wykoff for suggesting quick and accurate method used to record the atomic positions, to Dr. R. Diamond for sending us his model-building programme and to Mrs. M. Sawyer and Mrs. J. Denton for assistance in plotting the map and building the model. D.M.S. is grateful to the Beit Memorial Trust for financial support. We would also like to thank the Bristol Computer Centre and the Science Research Council for continued support. The optical comparator was built using funds provided by the Royal Society. REFERENCES 1. 2. 3. 4. 5.
6. 7. 8. 9. 10.
Shotton, D.M. and Watson, H.C., Phil. Trnas. Roy. Sot. Lond. B, 257, 111 (1970). Watson, H.C., Shotton, D.M., Cox, J.C. and Muirhead, H., Nature, 225, 806 (1970). Shotton, D.M. and Watson, H.C., Nature, 225, 811 (1970). Shotton, D.M., White, N.J. and Watson, H.C., Cold Spring Harbor Symp. Quant. Biol., 36, 91 (1971). Shotton, D.M. and Hartley, B.S., Nature, 225, 802 (1970). Richards, F.M., J. Mol. Biol., 37, 225 (1968). Colman, P.M., Jansonius, J.N. and Matthews, B.W., J. Mol. Biol., 2, 701 (1972). Salemme, F.R. and Fehr, D.G., J. Mol. Biol., 2, 697 (1972). IUPAC-IUB Commission on Biochemical Nomenclature, J. Mol. Biol., 52, 1 (19701. Diamond, R., Acta Cryst., 21, 253 (1966).
951
BIOCHEMICAL
ATOMIC
Molecular Medical
Received
D.M.
Enzymology
Laboratory,
School,
accurate
Department
of Biochemistry,
Bristol,
set of non-hydrogen, given. This includes
2, 3).
BS8 lTD,
England.
model
atomic coordinates of porcine the tosyl group and the internal
pancreatic
elastase
Recently,
determination
atomic
Watson*
1973
(1,
structure
and H.C.
Walk,
of porcine
resolution
RESEARCH COMMUNICATIONS
FOR TOSYL-ELASTASE
Shotto
University
June 1,
The structure
the
COORDINATES
L. Sawyer,
Summary: The full tosyl elastase is water molecules.
3.52
AND BIOPHYSICAL
we have
extended
of tosyl-elastase
of the enzyme,
has been
to 2.52
the
coordinates
the
determined
at
resolution
of
and have built of which
are
an reported
here. High
resolution
derivatives new data
uously
as were were
reflexions
X-ray
positions
of the membered obvious. +
*
Present
To
density
of almost
representing
the
Sulphur
appears
clearly
side
and forking atoms
address:
chains
Copyrikht @ 1973 by Academic &-es, AN rights of reproduction in any form
Jnc. reserved.
of merit
from
being
these
0.86
in a clear
same
for
protrusions
clear,
with
side-chains
of Botany, California
are
the
Dimpling is, just
for
the Density exception
of sixthe most part,
resolved
University of California, 94720, U.S.A.
be addressed.
944
atoms.
residues.
bridges
indicating
oxygen
all
and unambig-
the map as a continuous
is also
polar
of disulphide
should
obtained
resulted
carbonyl
of branched
Department Berkeley,
whom correspondence
in
defined
of some surface
of the
map.
of the peptide
amino-acid
The phases
and this
density
chain
with all
extremities rings
and 2.51,
main
from crystals,
the mean figure
electron
The polypeptide of high
collected (2).
accuracy,
3.64x
interpretable
ribbon
were
used previously
of high
between
data
and
Vol. 53, No. 3,1973
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
.OlSr
0a c
65
95 Dlstonce -re
at twice
the main-chain
can be identified determined Asn-186
from
primary is very
the density
associated
tosyl
attached
group
sulphate
ion
are also
well
Using
alone,
is known
to deamidation
with
five
as a function of indicate the points
internal
confirming
indeed,
an aspartic
peaks centre
of the
from the
and,
with
protein,
to the active twenty
the
sequence
chemically work
the electron acid.
representing serine
residues
residue,
and many surface
that density
In addition
the positions
to of the
a surface-bound water
molecules,
(6,7),
a model
defined.
an optical
comparator
with
a vertical
from Kendrew-Watson
Engineers,
the electron
It
is more consistent
(4),
constructed
Repetition
of all
5
in cm
The majority
density
(5).
susceptible
point
density.
the electron
structure
map at that
been
35 mlrrcw
The mean error in the x-coordinate plotted the distance from the mirror. Error bars averaged over less than 100 observations.
I
appear
from
density
non-hydrogen
Greens
Road,
skeletal Cambridge,
map of tosyl-elastase. atoms
including
those
TABLE l(see
mirror components
has
(Cambridge
England)
which
fits
accurately
From this
model,
the coordinates
of the tosyl
group,
sulphate
ion
and
pp. 946-951) The measured coordinates are recorded in gngstrom units (O.lnm) measured from the origin of the unit cell (P2I2 2 ), along the crystallographic axes. Amino-acid residues are identified by 1 heir l. number in the chymotrypsinogen-A numbering scheme (5) to facilitate comparison. Atoms are identified according to the IUPAC-IUB conventions, 1970 (9) using Latin equivalents of Greek characters. ll has been transliterated as EH rather than H. The positions of the amino group and oxygen atom of amide side-chains have been determined from stereochemical considerations. An asterisk preceding an atomic coordinate indicates that that atom is not clearly visible in the electron rotating surface residues and density map. Such atoms belong to freely were built fully staggered.
945
Vol. 53, No. 3,1973
BIOCHEMICAL
CB
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BIOCHEMICAL
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Vol. 53, No. 3, 1973
BlOCHEMlCAt
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
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BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
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BIOCHEMICAL
Vol. 53, No. 3, 1973
HAT
16
MIT
-1.9
OH2
20.2
45.6
YLT 17 OH2 Y4T
29.3
-9.b
19
OH2 IdAT 20
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on2
-9.9
56.1 WIT
18
on2
-?.I
internal
28.5
54.7
waters
described Gross
clerical
the output between
errors from
perpendicular
was 0.1881.
18.8
description
5.1
Y41
OH2 23 on2 21
4.4
35.1
30.2
U4f
on2
2.2
Sb.8
38.b
51.1
using
WIT
have
(10).
and those
obtained
of depth
produces as is
and its
57.8
31.1
so4
-8.5
21.8
68.9
of the device as measured.
been eliminated
using
deviation
by the model-building in the direction
variation
shown in Figure
of the structure
9.2
1
coordinates
The r.m.s.
perception
a systematic
25
on2
version the
programme
The problem
41.2 SUL
1 lists
measurement
coordinates
36.1
a simplified
Table
(8).
measurement
22
48.3
in coordinate
to the mirror
of the x-coordinate A full
and Fehr
MIT
46.4
19.6
a model-building
the measured
programme
18.6
have been measured
by Salemmi
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
in
the accuracy
I.
determination
is
in
preparation to us the We are grateful to Professor H. Wykoff for suggesting quick and accurate method used to record the atomic positions, to Dr. R. Diamond for sending us his model-building programme and to Mrs. M. Sawyer and Mrs. J. Denton for assistance in plotting the map and building the model. D.M.S. is grateful to the Beit Memorial Trust for financial support. We would also like to thank the Bristol Computer Centre and the Science Research Council for continued support. The optical comparator was built using funds provided by the Royal Society. REFERENCES 1. 2. 3. 4. 5.
6. 7. 8. 9. 10.
Shotton, D.M. and Watson, H.C., Phil. Trnas. Roy. Sot. Lond. B, 257, 111 (1970). Watson, H.C., Shotton, D.M., Cox, J.C. and Muirhead, H., Nature, 225, 806 (1970). Shotton, D.M. and Watson, H.C., Nature, 225, 811 (1970). Shotton, D.M., White, N.J. and Watson, H.C., Cold Spring Harbor Symp. Quant. Biol., 36, 91 (1971). Shotton, D.M. and Hartley, B.S., Nature, 225, 802 (1970). Richards, F.M., J. Mol. Biol., 37, 225 (1968). Colman, P.M., Jansonius, J.N. and Matthews, B.W., J. Mol. Biol., 2, 701 (1972). Salemme, F.R. and Fehr, D.G., J. Mol. Biol., 2, 697 (1972). IUPAC-IUB Commission on Biochemical Nomenclature, J. Mol. Biol., 52, 1 (19701. Diamond, R., Acta Cryst., 21, 253 (1966).
951