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PDBsum entry 1bit
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Serine proteinase
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PDB id
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1bit
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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 anionic salmon trypsin in a second crystal form.
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Authors
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G.I.Berglund,
A.O.Smalås,
A.Hordvik,
N.P.Willassen.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1995,
51,
725-730.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
88%.
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Abstract
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Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at
1.83 A, resolution. The crystals are orthorhombic and belong to space group
P2(1)2(1)2 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 A. The
present structure has been compared to salmon trypsin as it appears in a
previously reported crystal form (ST-IIA) with cell dimensions a = 61.95, b =
84.33 and c = 39.11 A [Smalås & Hordvik (1993). Acta Cryst. D49, 318-330].
The presence of a sulfate group involved in several hydrogen bonds to
active-site residues, and the location of an additional benzamidine site in the
crystal lattice, are the most striking differences between the present and the
previous structure. Superposition of main-chain atoms in the two structures give
an overall r.m.s. difference of 0.26 A, with the main differences located to
areas with different molecular packing. The overall coordinate error is
estimated to be between 0.20 and 0.25 A, by the method of Luzzati.
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Figure 3.
Fig. 3. Stereo drawing showing location of the sulfate ion, the two
benzamidine molecules and the calcium ion in the three-dimensional
structure of ST-lIB. C(~ backbone is drawn wit thin lines while side-
chain atoms of the catalytic triad residues (His57, Aspl02, Ser195)
and Asp189 at the base of the specificity pocket, the sulfate ion and
benzamidne molecules are drawn in thick lines. he calcium ion
is indicated by a sphere. ZA246 is in the specficity pocket while
BZA247 is located at the surface of the protein mediating contacts to
a neighbouring molecule.
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Figure 4.
Fig. 4. Stereoview showing density for a benzamidine molecule at
two sites. The electron density corresponds to 2Fo-Fc with the
benzamidine molecule omitted from the calculations. The maps are
contoured at 1.5a level. (a) Benzamidine bound in the specificity
pocket of ST-IIB with corresponding hydrogen-bonding pattern. (b)
Benzamidine molecule mediating intermolecular contacts at the exten-
sion of the primary binding site. Posible hydrogen bonds to Serl71 O
and Asn224 N62 are inicated with broken lines. Residues Thr#76 and
Phe#82 are from a neighbouring molecule.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1995,
51,
725-730)
copyright 1995.
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Secondary reference #1
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Title
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Cold adaption of enzymes: structural comparison between salmon and bovine trypsins.
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Authors
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A.O.Smalås,
E.S.Heimstad,
A.Hordvik,
N.P.Willassen,
R.Male.
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Ref.
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Proteins, 1994,
20,
149-166.
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above were
obtained from the PDBe's
server.
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Secondary reference #2
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Title
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Crystal structure determination and refinement of benzamidine-Inhibited trypsin from the north atlantic salmon (salmo salar)
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Authors
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A.O.Smalas,
A.Hordvik.
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Ref.
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acta crystallogr ,sect d, 1993,
49,
318.
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Secondary reference #3
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Title
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Crystallization and preliminary X-Ray crystallographic studies of benzamidine-Inhibited trypsin from the north atlantic salmon (salmo salar).
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Authors
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A.O.Smalås,
A.Hordvik,
L.K.Hansen,
E.Hough,
K.Jynge.
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Ref.
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J Mol Biol, 1990,
214,
355-358.
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PubMed id
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Secondary reference #4
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Title
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Crystal structure of bovine beta-Trypsin at 1.5 a resolution in a crystal form with low molecular packing density. Active site geometry, Ion pairs and solvent structure.
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Authors
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H.D.Bartunik,
L.J.Summers,
H.H.Bartsch.
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Ref.
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J Mol Biol, 1989,
210,
813-828.
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PubMed id
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Secondary reference #5
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Title
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The geometry of the reactive site and of the peptide groups in trypsin, Trypsinogen and its complexes with inhibitors
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Authors
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M.Marquart,
J.Walter,
J.Deisenhofer,
W.Bode,
R.Huber.
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Ref.
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acta crystallogr ,sect b, 1983,
39,
480.
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Secondary reference #6
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Title
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The accuracy of refined protein structures: comparison of two independently refined models of bovine trypsin
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Authors
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J.H.Chambers,
R.M.Stroud.
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Ref.
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acta crystallogr ,sect b, 1979,
35,
1861.
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