1omd: Difference between revisions

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[[Image:1omd.jpg|left|200px]]<br /><applet load="1omd" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1omd.jpg|left|200px]]<br /><applet load="1omd" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1omd, resolution 1.85Å" />

'''STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+'''<br />

==Overview==

The crystal structure of oncomodulin, a 12,000 Mr protein isolated from, rat tumours, has been determined by molecular replacement using the carp, parvalbumin structure as a starting model. Refinement was performed by, cycles of molecular fitting and restrained least-squares, using, area-detector intensity data to 1.85 A resolution. For the 5770, reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes, residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin, molecule. The oncomodulin backbone is closely related to that of, parvalbumin; however, some differences are found after a least-squares fit, of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2, A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall, r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the, two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to, seven oxygen atoms, including one water molecule. The third Ca2+ is also, seven-co-ordinated, to five oxygen atoms belonging to three different, oncomodulin molecules and to two water molecules which form hydrogen bonds, to a fourth oncomodulin; thus, this intermolecular Ca2+ and its, equivalents interlink the molecules into zigzag layers normal to the b, axis with a spacing of b/2 or 32.14 A. No such extensive molecular, aggregation has been reported for any of the related Ca-binding regulatory, proteins of the troponin-C family studied thus far. The Ca-O distances in, all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly, bound Ca polyhedra.

The crystal structure of oncomodulin, a 12,000 Mr protein isolated from rat tumours, has been determined by molecular replacement using the carp parvalbumin structure as a starting model. Refinement was performed by cycles of molecular fitting and restrained least-squares, using area-detector intensity data to 1.85 A resolution. For the 5770 reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin molecule. The oncomodulin backbone is closely related to that of parvalbumin; however, some differences are found after a least-squares fit of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2 A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to seven oxygen atoms, including one water molecule. The third Ca2+ is also seven-co-ordinated, to five oxygen atoms belonging to three different oncomodulin molecules and to two water molecules which form hydrogen bonds to a fourth oncomodulin; thus, this intermolecular Ca2+ and its equivalents interlink the molecules into zigzag layers normal to the b axis with a spacing of b/2 or 32.14 A. No such extensive molecular aggregation has been reported for any of the related Ca-binding regulatory proteins of the troponin-C family studied thus far. The Ca-O distances in all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly bound Ca polyhedra.

==About this Structure==

1OMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1OMD OCA].

1OMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMD OCA].

==Reference==

Line 13:

[[Category: Rattus norvegicus]]

[[Category: Single protein]]

[[Category: Ahmed, F.R.]]

[[Category: Ahmed, F R.]]

[[Category: Birnbaum, G.I.]]

[[Category: Birnbaum, G I.]]

[[Category: Macmanus, J.P.]]

[[Category: Macmanus, J P.]]

[[Category: Pippy, M.E.]]

[[Category: Pippy, M E.]]

[[Category: Przybylska, M.]]

[[Category: Rose, D.R.]]

[[Category: Rose, D R.]]

[[Category: CA]]

[[Category: calcium binding protein]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Tue Nov 20 23~~:00:~~24 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:19:21 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1omd.jpg|left|200px]]<br /><applet load="1omd" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1omd.jpg|left|200px]]<br /><applet load="1omd" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1omd, resolution 1.85&Aring;" />
 '''STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+'''<br />
 ==Overview==
-The crystal structure of oncomodulin, a 12,000 Mr protein isolated from, rat tumours, has been determined by molecular replacement using the carp, parvalbumin structure as a starting model. Refinement was performed by, cycles of molecular fitting and restrained least-squares, using, area-detector intensity data to 1.85 A resolution. For the 5770, reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes, residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin, molecule. The oncomodulin backbone is closely related to that of, parvalbumin; however, some differences are found after a least-squares fit, of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2, A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall, r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the, two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to, seven oxygen atoms, including one water molecule. The third Ca2+ is also, seven-co-ordinated, to five oxygen atoms belonging to three different, oncomodulin molecules and to two water molecules which form hydrogen bonds, to a fourth oncomodulin; thus, this intermolecular Ca2+ and its, equivalents interlink the molecules into zigzag layers normal to the b, axis with a spacing of b/2 or 32.14 A. No such extensive molecular, aggregation has been reported for any of the related Ca-binding regulatory, proteins of the troponin-C family studied thus far. The Ca-O distances in, all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly, bound Ca polyhedra.
+The crystal structure of oncomodulin, a 12,000 Mr protein isolated from rat tumours, has been determined by molecular replacement using the carp parvalbumin structure as a starting model. Refinement was performed by cycles of molecular fitting and restrained least-squares, using area-detector intensity data to 1.85 A resolution. For the 5770 reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin molecule. The oncomodulin backbone is closely related to that of parvalbumin; however, some differences are found after a least-squares fit of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2 A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to seven oxygen atoms, including one water molecule. The third Ca2+ is also seven-co-ordinated, to five oxygen atoms belonging to three different oncomodulin molecules and to two water molecules which form hydrogen bonds to a fourth oncomodulin; thus, this intermolecular Ca2+ and its equivalents interlink the molecules into zigzag layers normal to the b axis with a spacing of b/2 or 32.14 A. No such extensive molecular aggregation has been reported for any of the related Ca-binding regulatory proteins of the troponin-C family studied thus far. The Ca-O distances in all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly bound Ca polyhedra.
 ==About this Structure==
-OMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OMD OCA].
+OMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMD OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Rattus norvegicus]]
 [[Category: Single protein]]
-[[Category: Ahmed, F.R.]]
+[[Category: Ahmed, F R.]]
-[[Category: Birnbaum, G.I.]]
+[[Category: Birnbaum, G I.]]
-[[Category: Macmanus, J.P.]]
+[[Category: Macmanus, J P.]]
-[[Category: Pippy, M.E.]]
+[[Category: Pippy, M E.]]
 [[Category: Przybylska, M.]]
-[[Category: Rose, D.R.]]
+[[Category: Rose, D R.]]
 [[Category: CA]]
 [[Category: calcium binding protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:00:24 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:19:21 2008''