1nxd: Difference between revisions

Revision as of 15:11, 21 February 2008

Crystal structure of MnMn Concanavalin A

OverviewOverview

Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The structure was solved at 1.9 angstroms, with free R and R values of 0.201 and 0.184, respectively. As expected, no molecules of the ligand were bound to the protein. Soaking in the cryobuffer left its fingerprint as 25 molecules of glycerol in the bound solvent, most of them at specific positions. The fact that a glycerol molecule is located in the sugar-binding pocket of each of the four subunits in the asymmetric unit and another is located in two of the peptide-binding sites suggests a recognition phenomenon rather than a displacement of water molecules by glycerol. Crystal contact analysis shows that a relation exists between the residues that form hydrogen bonds to other asymmetric units and the space group: contact Asp58-Ser62 is a universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and Tyr100-His205 contacts are general features of the C222(1) crystal form.

About this StructureAbout this Structure

1NXD is a Single protein structure of sequence from Canavalia ensiformis with , , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Structure of concanavalin A at pH 8: bound solvent and crystal contacts., Lopez-Jaramillo FJ, Gonzalez-Ramirez LA, Albert A, Santoyo-Gonzalez F, Vargas-Berenguel A, Otalora F, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1048-56. Epub 2004, May 21. PMID:15159564

Page seeded by OCA on Thu Feb 21 14:11:08 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1nxd.gif|left|200px]]<br /><applet load="1nxd" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1nxd.gif|left|200px]]<br /><applet load="1nxd" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1nxd, resolution 1.9&Aring;" />
 '''Crystal structure of MnMn Concanavalin A'''<br />
 ==Overview==
-Concanavalin A has been crystallized in the presence of the ligand, (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are, isomorphous to those reported for ConA complexed with peptides at low, resolution (3.00-2.75 angstroms). The structure was solved at 1.9, angstroms, with free R and R values of 0.201 and 0.184, respectively. As, expected, no molecules of the ligand were bound to the protein. Soaking in, the cryobuffer left its fingerprint as 25 molecules of glycerol in the, bound solvent, most of them at specific positions. The fact that a, glycerol molecule is located in the sugar-binding pocket of each of the, four subunits in the asymmetric unit and another is located in two of the, peptide-binding sites suggests a recognition phenomenon rather than a, displacement of water molecules by glycerol. Crystal contact analysis, shows that a relation exists between the residues that form hydrogen bonds, to other asymmetric units and the space group: contact Asp58-Ser62 is a, universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and, Tyr100-His205 contacts are general features of the C222(1) crystal form.
+Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The structure was solved at 1.9 angstroms, with free R and R values of 0.201 and 0.184, respectively. As expected, no molecules of the ligand were bound to the protein. Soaking in the cryobuffer left its fingerprint as 25 molecules of glycerol in the bound solvent, most of them at specific positions. The fact that a glycerol molecule is located in the sugar-binding pocket of each of the four subunits in the asymmetric unit and another is located in two of the peptide-binding sites suggests a recognition phenomenon rather than a displacement of water molecules by glycerol. Crystal contact analysis shows that a relation exists between the residues that form hydrogen bonds to other asymmetric units and the space group: contact Asp58-Ser62 is a universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and Tyr100-His205 contacts are general features of the C222(1) crystal form.
 ==About this Structure==
-NXD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis] with AZI, MN, NA and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NXD OCA].
+NXD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis] with <scene name='pdbligand=AZI:'>AZI</scene>, <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXD OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Albert, A.]]
-[[Category: Gonzalez-Ramirez, L.A.]]
+[[Category: Gonzalez-Ramirez, L A.]]
-[[Category: Lopez-Jaramillo, F.J.]]
+[[Category: Lopez-Jaramillo, F J.]]
 [[Category: Otalora, F.]]
 [[Category: Santoyo-Gonzalez, F.]]
@@ Line 25: / Line 25: @@
 [[Category: lectin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:38:30 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:11:08 2008''