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References listed in PDB file
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Key reference
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Title
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Structures of product and inhibitor complexes of streptomyces griseus protease a at 1.8 a resolution. A model for serine protease catalysis.
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Authors
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M.N.James,
A.R.Sielecki,
G.D.Brayer,
L.T.Delbaere,
C.A.Bauer.
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Ref.
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J Mol Biol, 1980,
144,
43-88.
[DOI no: ]
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PubMed id
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Abstract
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No abstract given.
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Figure 3.
FIG:. 3. Difference electron density maps computed with coefficients IE',\ - IP,I. phases hC in the region
ofthe active ite of SGPA. These are fragment maps in which a portin of the molecule was not included in.~
the structure factor calculation.
(a) AcPro-Ala-Pro-Phe-OH, peptide 1, the atoms excluded from the phase calculation were 0' of
Ser195 and th terminal carboxyl oxygen atom of the tetrapeptide product which binds in the oxyanion
bindin site. The 2 largest positive peaks correspond to these expected atomic position. The 3rd peak
just below that for OY of Ser195 corresponds to a water molecule not included in the phasng.
(b) The corresponding atomic model ofthe tetrapeptide aldehyde (onl P, Pro and P, Phe shown) with
the electron ensity for Oy Her195 and the two water moleules 0366 and 0361 which were not mcluded in
the calculation.
In both (a) and (b) the electron density cotour surfaces are kO.23 eA3 and the negative density is
represented by broken lines. This and subsequent Figures have been made with the aid of the MMS-X
interactive graphics (Barry et al., 1976).
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Figure 9.
FIG. 9. Comparison ofthe binding modes ofthe Ac-Pro-Ala-Pro-Phe-OH product (solid, thin lines) and
the aldehyde inhibitor (broken lines). The enzyme conformation is that obseved in complex I. The P, Pro
ring hs a changed coformation in the aldehyde. The carbonyl carbon atom of the aldehyde is I.73 A
distant from Oy of Ser195.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1980,
144,
43-88)
copyright 1980.
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Secondary reference #1
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Title
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The importance of refined structures to the understanding of enzyme action
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Authors
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A.R.Sielecki,
M.N.G.James.
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Ref.
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proceedings of the daresbury ...
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Secondary reference #2
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Title
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Protein structure refinement: streptomyces griseus serine protease a at 1.8 a resolution.
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Authors
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A.R.Sielecki,
W.A.Hendrickson,
C.G.Broughton,
L.T.Delbaere,
G.D.Brayer,
M.N.James.
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Ref.
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J Mol Biol, 1979,
134,
781-804.
[DOI no: ]
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PubMed id
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Figure 1.
FIG. I(a). Electron density map computed with coefficients 2 [E,,[ -- iP,j and caculated phsuou,
a,, after Ieast-squares cycle 19 (Table 4) for the C-termnal region of Lsu242. The mdecular
models of II6124 (1124) and Leu242 (L242) are shown superimposed on the electron density
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Figure 10.
FIG. 10. The co-ordination octahedron of the 6 closest oxygen atoms to the sodium ion in the
vicinity f th carboxylate of eu242. The 4, crystallographic axis of the space group is concident
with the line joining water molecules 0222 and 0236. The 2 resulting octahedra share a common
edge. The bond istances rom the Na
to 2.83 A.
+ ion to the 6 co-ordinating oxygen atoms range from 2.30
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease a at 1.5 a resolution.
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Authors
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J.Moult,
F.Sussman,
M.N.James.
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Ref.
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J Mol Biol, 1985,
182,
555-566.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Schematic representation of the definition of
depth below the protein suface used or atoms with
greater than a minimum specified solvent accessiblity
(class A).
The slab represents the protein surfce surrounding an
atom. The fractional solvent accessibility f o an atom of
radius R for te real protein surface implies a depth D
below uch a hypothetical slab surface.
Protruding Eap: area, A,. Atom at surface: area, A,;
radius, R.
Fractional accessibility, f = A,/A,. Depth, D = R-2fR
(D = 0 forf= 0.5).
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Figure 9.
igure 9. Environmentl perturbation map of the
His57 and Asp102 side-chain models for the uncharged
state of the histidine. Contouring as in the other EP
maps. There is a depletion of density in t,he lone pail
region of the N&2 atom of the histidine.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #4
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Title
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Crystallographic and kinetic investigations of the covalent complex formed by a specific tetrapeptide aldehyde and the serine protease from streptomyces griseus.
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Authors
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G.D.Brayer,
L.T.Delbaere,
M.N.James,
C.A.Bauer,
R.C.Thompson.
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Ref.
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Proc Natl Acad Sci U S A, 1979,
76,
96.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Molecular structure of crystalline streptomyces griseus protease a at 2.8 a resolution. Ii. Molecular conformation, Comparison with alpha-Chymotrypsin and active-Site geometry.
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Authors
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G.D.Brayer,
L.T.Delbaere,
M.N.James.
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Ref.
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J Mol Biol, 1978,
124,
261-283.
[DOI no: ]
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PubMed id
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Figure 4.
Fro. 4. Schematic rawing of the observed secondary structural features of SGPA. Hydrogen
onds betwen main-chain carbonyl oxygen and imino nitrogen atoms are indicated. The residue
numbering is that of the sequence alignment in Table 1. (0) Charged acidic residues; (A) basic
groups; (0) hydrophilic uncharged; and ( n ) hydrophobic. The 2 disulfide bridges arc shown a<
thick lines. The tertiary structural features of the main chain are shown in Figure 5.
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Figure 9.
FIQ. 9. The environment of the N-terminus of SGPA showing how it is accessible to protonation
or acetylation without affecting the catalytic machinery of this enzyme. The a-amino group points
towards a slvent cavity whereas the set-butyl side-chain is in the hydrophobic core of the N-
terminal domain. See Fig. 7(a) for the overall placement of this residue.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #6
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Title
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Molecular structure of crystalline streptomyces griseus protease a at 2.8 a resolution. I. Crystallization, Data collection and structural analysis.
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Authors
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G.D.Brayer,
L.T.Delbaere,
M.N.James.
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Ref.
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J Mol Biol, 1978,
124,
243-259.
[DOI no: ]
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PubMed id
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Figure 3.
FIQ. 3. Heavy-atom difference Patterson maps for the 3 majr derivatives used in this study:
(a) sodium mersslyl, (b) mercury chloranilste and (c) rhenium trichloride. The 2 Harker sections
w =- 0 and w = 4 are shown or each derivative. Crosses mark the positions of refined heavy-atom
sites that were initially determined from these Patterson maps. Only the mercury chloranilate
derivative has more han one heavy-atom binding site. u, v and w in Patt,erson space corresponcl
to o, b and c of the crystallographic unit cell.
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Figure 6.
FIQ. 6. The distribution of the figres-of-merit amng native enzyme reflections phased using
the isomorphous replacement technique. The percentge of the total reflectiona falling into eech
range is shown at the top of each column. The broken line indicates the overall mean figure-of-
merit for all reflections.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #7
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Title
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Amino acid sequence alignment of bacterial and mammalian pancreatic serine proteases based on topological equivalences.
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Authors
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M.N.James,
L.T.Delbaere,
G.D.Brayer.
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Ref.
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Can J Biochem, 1978,
56,
396-402.
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PubMed id
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Secondary reference #8
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Title
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Tertiary structural differences between microbial serine proteases and pancreatic serine enzymes.
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Authors
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L.T.Delbaere,
W.L.Hutcheon,
M.N.James,
W.E.Thiessen.
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Ref.
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Nature, 1975,
257,
758-763.
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PubMed id
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Secondary reference #9
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Title
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Structure of the complex formed between the bacterial-Produced inhibitor chymostatin and the serine enzyme streptomyces griseus protease a.
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Authors
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L.T.Delbaere,
G.D.Brayer.
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Ref.
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J Mol Biol, 1980,
139,
45-51.
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PubMed id
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Secondary reference #10
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Title
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Refined structure of alpha-Lytic protease at 1.7 a resolution. Analysis of hydrogen bonding and solvent structure.
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Authors
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M.Fujinaga,
L.T.Delbaere,
G.D.Brayer,
M.N.James.
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Ref.
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J Mol Biol, 1985,
184,
479-502.
[DOI no: ]
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PubMed id
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Figure 8.
Figure 8. (a) The region around &-Pro95 that is in a reverse open turn conformation (Ramachandran & Mitra, 1976).
(Hydrogen bonds are shown by broken lines.) (b) The homologous region in SGPA is shown (continuous line and abeled
residues) superimposed on the equivalent residues of a-lytic rotease broken lines). The superposition was done using ll
the a-carbons in each molecule.
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Figure 14.
Figure 14. Hydrogen-onding involving the buried chrged residues Arg138 and Asp194. The boken lines show theFigure 14. Hydrogen-onding involving the buried chrged residues Arg138 and Asp194. The boken lines show the
ydrogen bonds. 02 is a tightly bonded internal water molecule. The interaction between the charged residues isydrogen bonds. 02 is a tightly bonded internal water molecule. The interaction between the charged residues is
mediated by Thr143.mediated by Thr143.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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