1a6n: Difference between revisions

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DEOXY-MYOGLOBIN, ATOMIC RESOLUTION

OverviewOverview

We have used x-ray crystallography to determine the structures of sperm whale myoglobin (Mb) in four different ligation states (unligated, ferric aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better than 1.2 A. Data collection and analysis were performed in as much the same way as possible to reduce model bias in differences between structures. The structural differences among the ligation states are much smaller than previously estimated, with differences of <0.25 A root-mean-square deviation among all atoms. One structural parameter previously thought to vary among the ligation states, the proximal histidine (His-93) azimuthal angle, is nearly identical in all the ferrous complexes, although the tilt of the proximal histidine is different in the unligated form. There are significant differences, however, in the heme geometry, in the position of the heme in the pocket, and in the distal histidine (His-64) conformations. In the CO complex the majority conformation of ligand is at an angle of 18 +/- 3 degrees with respect to the heme plane, with a geometry similar to that seen in encumbered model compounds; this angle is significantly smaller than reported previously by crystallographic studies on monoclinic Mb crystals, but still significantly larger than observed by photoselection. The distal histidine in unligated Mb and in the dioxygenated complex is best described as having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in low-pH structures where His-64 is doubly protonated. We suggest that these conformations of the distal histidine correspond to the different conformational substates of MbCO and MbO(2) seen in vibrational spectra. Full-matrix refinement provides uncertainty estimates of important structural parameters. Anisotropic refinement yields information about correlated disorder of atoms; we find that the proximal (F) helix and heme move approximately as rigid bodies, but that the distal (E) helix does not.

About this StructureAbout this Structure

1A6N is a Single protein structure of sequence from Physeter catodon with and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structures of myoglobin-ligand complexes at near-atomic resolution., Vojtechovsky J, Chu K, Berendzen J, Sweet RM, Schlichting I, Biophys J. 1999 Oct;77(4):2153-74. PMID:10512835

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-[[Image:1a6n.gif|left|200px]]<br /><applet load="1a6n" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1a6n, resolution 1.15&Aring;" />
 '''DEOXY-MYOGLOBIN, ATOMIC RESOLUTION'''<br />
 ==Overview==
-We have used x-ray crystallography to determine the structures of sperm, whale myoglobin (Mb) in four different ligation states (unligated, ferric, aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better, than 1.2 A. Data collection and analysis were performed in as much the, same way as possible to reduce model bias in differences between, structures. The structural differences among the ligation states are much, smaller than previously estimated, with differences of &lt;0.25 A, root-mean-square deviation among all atoms. One structural parameter, previously thought to vary among the ligation states, the proximal, histidine (His-93) azimuthal angle, is nearly identical in all the ferrous, complexes, although the tilt of the proximal histidine is different in the, unligated form. There are significant differences, however, in the heme, geometry, in the position of the heme in the pocket, and in the distal, histidine (His-64) conformations. In the CO complex the majority, conformation of ligand is at an angle of 18 +/- 3 degrees with respect to, the heme plane, with a geometry similar to that seen in encumbered model, compounds; this angle is significantly smaller than reported previously by, crystallographic studies on monoclinic Mb crystals, but still, significantly larger than observed by photoselection. The distal histidine, in unligated Mb and in the dioxygenated complex is best described as, having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in, low-pH structures where His-64 is doubly protonated. We suggest that these, conformations of the distal histidine correspond to the different, conformational substates of MbCO and MbO(2) seen in vibrational spectra., Full-matrix refinement provides uncertainty estimates of important, structural parameters. Anisotropic refinement yields information about, correlated disorder of atoms; we find that the proximal (F) helix and heme, move approximately as rigid bodies, but that the distal (E) helix does, not.
+We have used x-ray crystallography to determine the structures of sperm whale myoglobin (Mb) in four different ligation states (unligated, ferric aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better than 1.2 A. Data collection and analysis were performed in as much the same way as possible to reduce model bias in differences between structures. The structural differences among the ligation states are much smaller than previously estimated, with differences of &lt;0.25 A root-mean-square deviation among all atoms. One structural parameter previously thought to vary among the ligation states, the proximal histidine (His-93) azimuthal angle, is nearly identical in all the ferrous complexes, although the tilt of the proximal histidine is different in the unligated form. There are significant differences, however, in the heme geometry, in the position of the heme in the pocket, and in the distal histidine (His-64) conformations. In the CO complex the majority conformation of ligand is at an angle of 18 +/- 3 degrees with respect to the heme plane, with a geometry similar to that seen in encumbered model compounds; this angle is significantly smaller than reported previously by crystallographic studies on monoclinic Mb crystals, but still significantly larger than observed by photoselection. The distal histidine in unligated Mb and in the dioxygenated complex is best described as having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in low-pH structures where His-64 is doubly protonated. We suggest that these conformations of the distal histidine correspond to the different conformational substates of MbCO and MbO(2) seen in vibrational spectra. Full-matrix refinement provides uncertainty estimates of important structural parameters. Anisotropic refinement yields information about correlated disorder of atoms; we find that the proximal (F) helix and heme move approximately as rigid bodies, but that the distal (E) helix does not.
 ==About this Structure==
-A6N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon] with SO4 and HEM as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1A6N OCA].
+A6N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6N OCA].
 ==Reference==
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 [[Category: Chu, K.]]
 [[Category: Schlichting, I.]]
-[[Category: Sweet, R.M.]]
+[[Category: Sweet, R M.]]
 [[Category: Vojtechovsky, J.]]
 [[Category: HEM]]
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 [[Category: oxygen transport]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:38:43 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:41:26 2008''