Journal:IUCrJ:S2052252522007497
From Proteopedia
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<scene name='91/919674/Cv3/2'>7k3t anomalous density map</scene>. When collecting X-ray diffraction data, heavy atoms have a property called anomalous scattering which helps us pinpoint their location within a crystal structure. This gives rise to anomalous electron density, which is present in the asymmetric unit for data collected for PDB entry [[7kt3]], above 4 σ in the vicinity of the active site (as shown here). This strong anomalous peak at the position in question for [[7k3t]] is critical, as these data were collected from the same batch of crystals as our reported multitemperature data sets, despite also having used an off-edge wavelength for Zn2+ during data collection. This not only allowed the identification of Zn2+ alternate conformations modeled in [[7k3t]], displaying tetrahedral coordination geometry (white dotted lines), but is extremely important to demonstrate definitive placement of Zn2+ in our multitemperature models. | <scene name='91/919674/Cv3/2'>7k3t anomalous density map</scene>. When collecting X-ray diffraction data, heavy atoms have a property called anomalous scattering which helps us pinpoint their location within a crystal structure. This gives rise to anomalous electron density, which is present in the asymmetric unit for data collected for PDB entry [[7kt3]], above 4 σ in the vicinity of the active site (as shown here). This strong anomalous peak at the position in question for [[7k3t]] is critical, as these data were collected from the same batch of crystals as our reported multitemperature data sets, despite also having used an off-edge wavelength for Zn2+ during data collection. This not only allowed the identification of Zn2+ alternate conformations modeled in [[7k3t]], displaying tetrahedral coordination geometry (white dotted lines), but is extremely important to demonstrate definitive placement of Zn2+ in our multitemperature models. | ||
| - | <scene name='91/919674/Cv4/26'>Overview of the local conformational shifts connecting the active site, interdomain interface, and dimer interface</scene>. | + | <scene name='91/919674/Cv4/26'>Overview of the local conformational shifts connecting the active site, interdomain interface, and dimer interface</scene>. The 240 K dataset is in cyan and the 100 K dataset is in dark blue. Ligands from cocrystal structures are shown <scene name='91/919674/Cv4/25'>at the active site</scene> (salmon, [[6lu7]]), interdomain interface (violet, [[5ree]]; yellow, [[5rec]]), and dimer interface (orange, [[7lfp]]; pink, [[5rf0]]). <scene name='91/919674/Cv4/6'>Conformational shifts at the dimer interface</scene>. At the dimer interface Glu290 switches from <scene name='91/919674/Cv4/7'>one side-chain rotamer at 100 K</scene> to <scene name='91/919674/Cv4/8'>two alternate rotamers at 240 K</scene>. Glu290 is spatially adjacent to Cys128, which switches from <scene name='91/919674/Cv4/9'>two alternate rotamers at 100 and 240 K</scene> to a single rotamer at 277 K and above in our multiconformer models; the alternate rotamer occupancy is lower at 240 K, consistent with its positive Fo - Fo peak. These residues are near <scene name='91/919674/Cv4/10'>two ligands from separate crystallographic screens</scene> ([[7lfp]] and [[5rf0]]), as well as many ordered PEG molecules from the crystallization cocktails of various structures ([[7kvr]], [[7kvl]], [[7kfi]], and [[7lfe]]). <span class="bg-yellow"><span class="far fa-hand-point-right"></span> Remember to drag the structures with the mouse to rotate them.</span> <scene name='91/919674/Cv4/12'>These two ligands bind at the dimer interface</scene> of the biological monomer, constituted in the crystal from a symmetry-related protomer (gray surface). This interface also includes the Asp197 region. |
<scene name='91/919674/Cv4/16'>At the interdomain interface</scene>, Thr198 switches from <scene name='91/919674/Cv4/17'>two alternate side-chain rotamers at 100 K</scene> to a <scene name='91/919674/Cv4/18'>single rotamer at 240 K</scene>, while <scene name='91/919674/Cv4/19'>Glu240 – located across the interdomain interface – changes side-chain rotamer</scene>, with additional effects on the adjacent backbone of Pro241. Meanwhile, an <scene name='91/919674/Cv4/27'>interacting water molecule at 100 K</scene> (blue sphere) <scene name='91/919674/Cv4/22'>becomes displaced at 240 K, and is correspondingly absent in that model</scene>. Two <scene name='91/919674/Cv4/23'>ligands are shown at the interdomain interface</scene> (violet, [[5ree]]; yellow, [[5rec]]). | <scene name='91/919674/Cv4/16'>At the interdomain interface</scene>, Thr198 switches from <scene name='91/919674/Cv4/17'>two alternate side-chain rotamers at 100 K</scene> to a <scene name='91/919674/Cv4/18'>single rotamer at 240 K</scene>, while <scene name='91/919674/Cv4/19'>Glu240 – located across the interdomain interface – changes side-chain rotamer</scene>, with additional effects on the adjacent backbone of Pro241. Meanwhile, an <scene name='91/919674/Cv4/27'>interacting water molecule at 100 K</scene> (blue sphere) <scene name='91/919674/Cv4/22'>becomes displaced at 240 K, and is correspondingly absent in that model</scene>. Two <scene name='91/919674/Cv4/23'>ligands are shown at the interdomain interface</scene> (violet, [[5ree]]; yellow, [[5rec]]). | ||
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