 |
PDBsum entry 1bhc
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Protease inhibitor
|
PDB id
|
|
|
|
1bhc
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
The decameric structure of bovine pancreatic trypsin inhibitor (bpti) crystallized from thiocyanate at 2.7 a resolution.
|
|
|
Authors
|
|
C.Hamiaux,
T.Prangé,
M.Riès-Kautt,
A.Ducruix,
S.Lafont,
J.P.Astier,
S.Veesler.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1999,
55,
103-113.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
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
83%.
|
|
|
|
Abstract
|
|
|
The structure of a monoclinic form of bovine pancreatic trypsin inhibitor (BPTI)
crystallized from a thiocyanate solution has been determined and refined at 2.7
A resolution. The space group is P21 with a = 71.56, b = 73.83, c = 64.47 A,
beta = 93.9 degrees and Z = 20. The ten independent molecules were located by a
multi-body molecular-replacement search as developed in the AMoRe program,
starting from a single monomer model (PDB code: 6PTI). The molecular arrangement
of the subunits is a decamer resulting from the combination of two orthogonal
fivefold and twofold non-crystallographic axes. This builds a globular
micelle-like particle which minimizes hydrophobic interactions with the solvent.
The refinement was conducted with non-crystallographic symmetry constraints up
to a final residual of R = 0.20 (Rfree= 0.26). The root-mean-square deviations
from ideal geometry were 0.015 A and 1.6 degrees on bond distances and bond
angles, respectively. Several sites for thiocyanate ions were analyzed.
|
|
|
|
|
|
|
|
Figure 5.
Figure 5 Least-squares fit of C  chains
of the ten subunits of the decamer, plus the three structures
4PTI, 5PTI and 6PTI crystallized in phosphate. The locations of
the binding zones of thiocyanates are indicated by dashed
circles with respect to this common target molecule. The two
phosphate anions of 5PTI and 6PTI structures are also reported -
they correspond to the anionic site 1. Due to
non-crystallographic symmetry considerations, the three anionic
sites correspond to four different binding zones. Site 1 and
site 1' are equivalent within each pentamer (molecules
SCN1-SCN3) e.g. thiocyanate-labelled SCN1 lies in site 1 for
subunit G and in site 1' for subunit F. Site 3 (SCN4-SCN7) is in
the vicinity of residues 47-49 of dimers A/F, B/J, C/I and E/G,
while site 4 (SCN8-SCN10) connects pairs of Lys46 from two
different pentamers: D/I, B/F and H/E.
|
|
Figure 7.
Figure 7 The surface of the BPTI decamer: the particle adopts a
micellar structure with most of the positively charged residues
pointing outwards and hydrophobic residues turned inside.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1999,
55,
103-113)
copyright 1999.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Comparison of solubilities and molecular interactions of bpti molecules giving different polymorphs
|
|
|
Authors
|
|
S.Lafont,
S.Veesler,
J.P.Astier,
R.Boistelle.
|
|
|
Ref.
|
|
j cryst growth, 1997,
173,
132.
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Structure of hexagonal turkey egg-White lysozyme at 1.65a resolution.
|
|
|
Author
|
|
P.L.Howell.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1995,
51,
654-662.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 1.
Fig. 1. Refinement of TEL. Plot of R factor versus the refinement process. The R factor is the cystallographic greement factor defined as
]F,+~ - F~l~[ ~ F,+~ where the observed quantities are measured reflection amplitudes and the calculated quantiies are computed from the
atomic coordinates of the current structural model. The starting moel for refinement was the previously determined pH 8 structure, PDB code:
3LZ2 (Howell, Almo, Parsons, Hajdu & Pelsko, 1992). Refinement steps 1-7 used the program X-PLOR and subsequnt refinement steps utilized
the least-squares refinement program PROFF7: ttigh-resolution data were included gradually over the ourse of the refinement as indicated in
the diagram. During steps 9-11 the data was temporarily truncated to 1.8 ,~ resolution. Steps 1(~11 represent several cycles of refinement and
manual rebuilding where the overall residual varied very little. The position of water molecule and their itermolecular interactions were being
checked. The number of water molecules in Fig. 1 represents the total number of water molecules at the nd of each refinemet cycle.
|
|
Figure 2.
Fig 2. Stereoview of the Ca representation of the refined structure of
turkey egg-white lysozyme. The olecule is oriented looking down
the first helix.
|
|
Figure 4.
Fig. 4. Stereoviews of ifference
Fouriers and a 2F,, - F,. electron-
density ap of the thiocyanate
ion used to determine the correct
orientation f the ion. For (a)-(c)
the maps were alculated with
the carbon atom excluded and
are contoured at 3cr. Positive
difference density is represented
by a solid line and negative
difference density by dashed
line. The diference ourier
maps were calculated with (a)
the N and S atoms represented
as two wter molecules, (b) with
N and S atoms in the correct
orientation and (c) the position
of the N and S atoms reversed.
(d) A 2Fo-F. e!cchun-density
map of the thiocyanate ion.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from the IUCr
|
|
|
Secondary reference #3
|
|
|
Title
|
|
Structure determination of a dimeric form of erabutoxin-B, Crystallized from a thiocyanate solution.
|
|
|
Authors
|
|
P.Saludjian,
T.Prangé,
J.Navaza,
R.Ménez,
J.P.Guilloteau,
M.Riès-Kautt,
A.Ducruix.
|
|
|
Ref.
|
|
Acta Crystallogr B, 1992,
48,
520-531.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor.
|
|
|
Authors
|
|
A.Wlodawer,
J.Deisenhofer,
R.Huber.
|
|
|
Ref.
|
|
J Mol Biol, 1987,
193,
145-156.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
