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PDBsum entry 2zr1
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Plant protein
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PDB id
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2zr1
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References listed in PDB file
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Key reference
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Title
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A biophysical elucidation for less toxicity of agglutinin than abrin-A from the seeds of abrus precatorius in consequence of crystal structure.
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Authors
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J.Cheng,
T.H.Lu,
C.L.Liu,
J.Y.Lin.
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Ref.
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J Biomed Sci, 2010,
17,
34-34.
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PubMed id
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Abstract
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X-ray crystal structure determination of agglutinin from Abrus precatorius in
Taiwan is presented. The crystal structure of agglutinin, a type II
ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in
Taiwan, has been determined from a novel crystalline form by the molecular
replacement method using the coordinates of abrin-a as the template. The
structure has space group P4(1)2(1)2 with Z = 8, and been refined at 2.6 A to
R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles
from the standard values are 0.009 A and 1.3 degrees. Primary, secondary,
tertiary and quaternary structures of agglutinin have been described and
compared with those of abrin-a to a certain extent. In subsequent docking
research, we found that Asn200 of abrin-a may form a critical hydrogen bond with
G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic
residue bound with the cleft in a more compact complementary relationship. This
may explain the lower toxicity of agglutinin than abrin-a, despite of similarity
in secondary structure and the activity cleft of two RIPs.
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Secondary reference #1
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Title
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Structure-Function analysis and insights into the reduced toxicity of abrus precatorius agglutinin i in relation to abrin.
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Authors
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A.Bagaria,
K.Surendranath,
U.A.Ramagopal,
S.Ramakumar,
A.A.Karande.
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Ref.
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J Biol Chem, 2006,
281,
34465-34474.
[DOI no: ]
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PubMed id
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Figure 9.
FIGURE 9. 2F[o] - F[c] omit maps around the Pro-199,
Tyr-73, and Tyr-112 residues (contoured at 1  ) are shown here.
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Figure 10.
FIGURE 10. A view down the crystallographic 2-fold axis of
the APA-I heterotetramer (A-B heterodimer). The schematic
representation shows the interacting A and A' subunits of two
A-B dimer, and the arrow shows the putative tetramerization
interface. The three arginine residues, namely Arg-125, Arg-134,
and Arg-181, are shown by ball and stick, and the corresponding
symmetry related residues have been omitted for clarity. The
disulfide bonds linking chain A and chain B are shown by ball
and stick model. The active site cleft is away from the
tetramerization interface.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #2
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Title
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Primary structure and function analysis of the abrus precatorius agglutinin a chain by site-Directed mutagenesis. Pro(199) of amphiphilic alpha-Helix h impairs protein synthesis inhibitory activity.
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Authors
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C.L.Liu,
C.C.Tsai,
S.C.Lin,
L.I.Wang,
C.I.Hsu,
M.J.Hwang,
J.Y.Lin.
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Ref.
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J Biol Chem, 2000,
275,
1897-1901.
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PubMed id
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Secondary reference #3
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Title
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Crystallization of agglutinin from the seeds of abrus precatorius.
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Authors
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K.Panneerselvam,
S.C.Lin,
C.L.Liu,
Y.C.Liaw,
J.Y.Lin,
T.H.Lu.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
898-899.
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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 abrin-A at 2.14 a.
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Authors
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T.H.Tahirov,
T.H.Lu,
Y.C.Liaw,
Y.L.Chen,
J.Y.Lin.
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Ref.
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J Mol Biol, 1995,
250,
354-367.
[DOI no: ]
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PubMed id
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Figure 7.
Figure 7. The electron density of the first sugar chain using the (Fo - Fc ) omit map contoured at 2.5 s.
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Figure 9.
Figure 9. Ramachandranplot of abrin-a. All residues of the A- and B-chains are included. The glycine residues are shown
as triangles. The percentage of residues with (f, 8) conformational angles in the most favoured regions (A, B, L) is 86.0%.
In additional allowed regions (0a, 0b, 0l, 0p) this percentage is 13.3%, and in the generously allowed regions (a,b,l,p)
it is 0.7%. Proline, glycine and the end residues are excluded from percentage calculations. In the generously allowed
regions, the labelled residues Asp35 belong to the A-chain, and Val2 and Ser5 belong to the B-chain.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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