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* Residue conservation analysis
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PDB id:
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Transport protein
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Title:
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Crystal structure of plasmodium yoelii multidrug resistance protein 2
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Structure:
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Transport protein. Chain: a, b, c, d. Engineered: yes
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Source:
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Plasmodium yoelii yoelii str. 17xnl. Organism_taxid: 352914. Strain: yoelii str. 17xnl. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.20Å
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R-factor:
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0.206
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R-free:
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0.288
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Authors:
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A.Dong,M.Gao,J.Choe,Y.Zhao,J.Lew,G.Wasney,Z.Alam,M.Melone, I.Kozieradzki,M.Vedadi,A.M.Edwards,C.H.Arrowsmith,J.Weigelt, M.Sundstrom,A.Bochkarev,R.Hui,J.D.Artz,Structural Genomics Consortium (Sgc)
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Key ref:
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M.Vedadi
et al.
(2007).
Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Mol Biochem Parasitol,
151,
100-110.
PubMed id:
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Date:
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27-Mar-06
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Release date:
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25-Apr-06
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PROCHECK
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Headers
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References
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Mol Biochem Parasitol
151:100-110
(2007)
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PubMed id:
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Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
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M.Vedadi,
J.Lew,
J.Artz,
M.Amani,
Y.Zhao,
A.Dong,
G.A.Wasney,
M.Gao,
T.Hills,
S.Brokx,
W.Qiu,
S.Sharma,
A.Diassiti,
Z.Alam,
M.Melone,
A.Mulichak,
A.Wernimont,
J.Bray,
P.Loppnau,
O.Plotnikova,
K.Newberry,
E.Sundararajan,
S.Houston,
J.Walker,
W.Tempel,
A.Bochkarev,
I.Kozieradzki,
A.Edwards,
C.Arrowsmith,
D.Roos,
K.Kain,
R.Hui.
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ABSTRACT
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Parasites from the protozoan phylum Apicomplexa are responsible for diseases,
such as malaria, toxoplasmosis and cryptosporidiosis, all of which have
significantly higher rates of mortality and morbidity in economically
underdeveloped regions of the world. Advances in vaccine development and drug
discovery are urgently needed to control these diseases and can be facilitated
by production of purified recombinant proteins from Apicomplexan genomes and
determination of their 3D structures. To date, both heterologous expression and
crystallization of Apicomplexan proteins have seen only limited success. In an
effort to explore the effectiveness of producing and crystallizing proteins on a
genome-scale using a standardized methodology, over 400 distinct Plasmodium
falciparum target genes were chosen representing different cellular classes,
along with select orthologues from four other Plasmodium species as well as
Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from
the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%)
crystallized, culminating in 36 crystal structures. These results demonstrate
that, contrary to previous findings, a standardized platform using Escherichia
coli can be effective for genome-scale production and crystallography of
Apicomplexan proteins. Predictably, orthologous proteins from different
Apicomplexan genomes behaved differently in expression, purification and
crystallization, although the overall success rates of Plasmodium orthologues do
not differ significantly. Their differences were effectively exploited to
elevate the overall productivity to levels comparable to the most successful
ongoing structural genomics projects: 229 of the 468 target genes produced
purified soluble protein from one or more organisms, with 80 and 32 of the
purified targets, respectively, leading to crystals and ultimately structures
from one or more orthologues.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.S.Halavaty,
Y.Kim,
G.Minasov,
L.Shuvalova,
I.Dubrovska,
J.Winsor,
M.Zhou,
O.Onopriyenko,
T.Skarina,
L.Papazisi,
K.Kwon,
S.N.Peterson,
A.Joachimiak,
A.Savchenko,
and
W.F.Anderson
(2012).
Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria.
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Acta Crystallogr D Biol Crystallogr,
68,
1359-1370.
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PDB codes:
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A.K.Wernimont,
M.Amani,
W.Qiu,
J.C.Pizarro,
J.D.Artz,
Y.H.Lin,
J.Lew,
A.Hutchinson,
and
R.Hui
(2011).
Structures of parasitic CDPK domains point to a common mechanism of activation.
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Proteins,
79,
803-820.
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PDB codes:
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J.D.Artz,
A.K.Wernimont,
J.E.Dunford,
M.Schapira,
A.Dong,
Y.Zhao,
J.Lew,
R.G.Russell,
F.H.Ebetino,
U.Oppermann,
and
R.Hui
(2011).
Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites.
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J Biol Chem,
286,
3315-3322.
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PDB codes:
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A.K.Wernimont,
J.D.Artz,
P.Finerty,
Y.H.Lin,
M.Amani,
A.Allali-Hassani,
G.Senisterra,
M.Vedadi,
W.Tempel,
F.Mackenzie,
I.Chau,
S.Lourido,
L.D.Sibley,
and
R.Hui
(2010).
Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
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Nat Struct Mol Biol,
17,
596-601.
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PDB codes:
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A.R.Cole,
L.P.Lewis,
and
H.Walden
(2010).
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex.
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Nat Struct Mol Biol,
17,
294-298.
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PDB code:
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J.A.Fernández-Robledo,
and
G.R.Vasta
(2010).
Production of recombinant proteins from protozoan parasites.
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Trends Parasitol,
26,
244-254.
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M.E.Victor,
A.Bengtsson,
G.Andersen,
D.Bengtsson,
J.P.Lusingu,
L.S.Vestergaard,
D.E.Arnot,
T.G.Theander,
L.Joergensen,
and
A.T.Jensen
(2010).
Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes.
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Malar J,
9,
325.
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M.Haffke,
A.Menzel,
Y.Carius,
D.Jahn,
and
D.W.Heinz
(2010).
Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
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Acta Crystallogr D Biol Crystallogr,
66,
979-987.
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PDB codes:
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M.S.Kimber,
A.Y.Yu,
M.Borg,
E.Leung,
H.S.Chan,
and
W.A.Houry
(2010).
Structural and theoretical studies indicate that the cylindrical protease ClpP samples extended and compact conformations.
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Structure,
18,
798-808.
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PDB code:
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M.Vedadi,
C.H.Arrowsmith,
A.Allali-Hassani,
G.Senisterra,
and
G.A.Wasney
(2010).
Biophysical characterization of recombinant proteins: a key to higher structural genomics success.
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J Struct Biol,
172,
107-119.
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P.K.Fyfe,
A.Dawson,
M.T.Hutchison,
S.Cameron,
and
W.N.Hunter
(2010).
Structure of Staphylococcus aureus adenylosuccinate lyase (PurB) and assessment of its potential as a target for structure-based inhibitor discovery.
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Acta Crystallogr D Biol Crystallogr,
66,
881-888.
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PDB code:
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R.Bakszt,
A.Wernimont,
A.Allali-Hassani,
M.W.Mok,
T.Hills,
R.Hui,
and
J.C.Pizarro
(2010).
The crystal structure of Toxoplasma gondii pyruvate kinase 1.
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PLoS One,
5,
e12736.
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PDB codes:
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S.D.Stojanović,
B.L.Zarić,
and
S.D.Zarić
(2010).
Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins.
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J Mol Model,
16,
1743-1751.
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A.Wernimont,
and
A.Edwards
(2009).
In situ proteolysis to generate crystals for structure determination: an update.
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PLoS ONE,
4,
e5094.
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G.J.Crowther,
A.J.Napuli,
A.P.Thomas,
D.J.Chung,
K.V.Kovzun,
D.J.Leibly,
L.J.Castaneda,
J.Bhandari,
C.J.Damman,
R.Hui,
W.G.Hol,
F.S.Buckner,
C.L.Verlinde,
Z.Zhang,
E.Fan,
and
W.C.van Voorhis
(2009).
Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands.
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J Biomol Screen,
14,
700-707.
|
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K.Vaughan,
M.Blythe,
J.Greenbaum,
Q.Zhang,
B.Peters,
D.L.Doolan,
and
A.Sette
(2009).
Meta-analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine-related issues.
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Parasite Immunol,
31,
78-97.
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M.Avril,
M.J.Hathaway,
M.M.Cartwright,
S.O.Gose,
D.L.Narum,
and
J.D.Smith
(2009).
Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris.
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Malar J,
8,
143.
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N.Pulicherla,
L.A.Pogorzala,
Z.Xu,
H.C.O Farrell,
F.N.Musayev,
J.N.Scarsdale,
E.A.Sia,
G.M.Culver,
and
J.P.Rife
(2009).
Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
|
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J Mol Biol,
391,
884-893.
|
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PDB codes:
|
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R.Alag,
N.Bharatham,
A.Dong,
T.Hills,
A.Harikishore,
A.A.Widjaja,
S.G.Shochat,
R.Hui,
and
H.S.Yoon
(2009).
Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C-terminal pentapeptide.
|
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Protein Sci,
18,
2115-2124.
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PDB code:
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W.Qiu,
A.Wernimont,
K.Tang,
S.Taylor,
V.Lunin,
M.Schapira,
S.Fentress,
R.Hui,
and
L.D.Sibley
(2009).
Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii.
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EMBO J,
28,
969-979.
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PDB codes:
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A.Smeets,
E.Loumaye,
A.Clippe,
J.F.Rees,
B.Knoops,
and
J.P.Declercq
(2008).
The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers.
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Protein Sci,
17,
700-710.
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PDB codes:
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B.M.Collins
(2008).
The structure and function of the retromer protein complex.
|
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Traffic,
9,
1811-1822.
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D.L.Doolan,
Y.Mu,
B.Unal,
S.Sundaresh,
S.Hirst,
C.Valdez,
A.Randall,
D.Molina,
X.Liang,
D.A.Freilich,
J.A.Oloo,
P.L.Blair,
J.C.Aguiar,
P.Baldi,
D.H.Davies,
and
P.L.Felgner
(2008).
Profiling humoral immune responses to P. falciparum infection with protein microarrays.
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Proteomics,
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4680-4694.
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E.A.Winzeler
(2008).
Malaria research in the post-genomic era.
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Nature,
455,
751-756.
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E.T.Larson,
W.Deng,
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A.Napuli,
N.Mueller,
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F.S.Buckner,
E.Fan,
A.Lauricella,
G.DeTitta,
J.Luft,
F.Zucker,
W.G.Hol,
C.L.Verlinde,
and
E.A.Merritt
(2008).
Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.
|
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J Mol Biol,
381,
975-988.
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PDB codes:
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H.C.O'Farrell,
Z.Xu,
G.M.Culver,
and
J.P.Rife
(2008).
Sequence and structural evolution of the KsgA/Dim1 methyltransferase family.
|
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BMC Res Notes,
1,
108.
|
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J.D.Artz,
J.E.Dunford,
M.J.Arrowood,
A.Dong,
M.Chruszcz,
K.L.Kavanagh,
W.Minor,
R.G.Russell,
F.H.Ebetino,
U.Oppermann,
and
R.Hui
(2008).
Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis.
|
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Chem Biol,
15,
1296-1306.
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PDB codes:
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J.Hinojosa-Moya,
B.Xoconostle-Cázares,
E.Piedra-Ibarra,
A.Méndez-Tenorio,
W.J.Lucas,
and
R.Ruiz-Medrano
(2008).
Phylogenetic and structural analysis of translationally controlled tumor proteins.
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J Mol Evol,
66,
472-483.
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J.Weigelt,
L.D.McBroom-Cerajewski,
M.Schapira,
Y.Zhao,
C.H.Arrowsmith,
and
C.H.Arrowmsmith
(2008).
Structural genomics and drug discovery: all in the family.
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Curr Opin Chem Biol,
12,
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L.M.Birkholtz,
G.Blatch,
T.L.Coetzer,
H.C.Hoppe,
E.Human,
E.J.Morris,
Z.Ngcete,
L.Oldfield,
R.Roth,
A.Shonhai,
L.Stephens,
and
A.I.Louw
(2008).
Heterologous expression of plasmodial proteins for structural studies and functional annotation.
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Malar J,
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M.S.Jurica
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Detailed close-ups and the big picture of spliceosomes.
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and
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The acidocalcisome as a target for chemotherapeutic agents in protozoan parasites.
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S.N.Moreno,
and
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Anti-infectives targeting the isoprenoid pathway of Toxoplasma gondii.
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T.Sawasaki,
M.Torii,
and
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Wheat germ cell-free system-based production of malaria proteins for discovery of novel vaccine candidates.
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S.Dimov,
A.Bochkarev,
and
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(2008).
First crystallographic models of human TBC domains in the context of a family-wide structural analysis.
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| |
Proteins,
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Y.Zhang,
M.Morar,
and
S.E.Ealick
(2008).
Structural biology of the purine biosynthetic pathway.
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| |
Cell Mol Life Sci,
65,
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G.Guncar,
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The use of Co2+ for crystallization and structure determination, using a conventional monochromatic X-ray source, of flax rust avirulence protein.
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PDB code:
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P.Gayathri,
H.Balaram,
and
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
