High diffraction quality crystals of cucurmosin, a type I ribosome inactivating protein isolated from the sarcocarp of Cucurbita moschata (pumpkin), have been grown under newly optimised conditions. With in-house rota...High diffraction quality crystals of cucurmosin, a type I ribosome inactivating protein isolated from the sarcocarp of Cucurbita moschata (pumpkin), have been grown under newly optimised conditions. With in-house rotating anode X-ray source, these crystals diffract to 1.65 ?resolution which is much higher than that of the previously reported crystals that diffracted only to 3 ?resolution. The crystals belong to space group P212121 with cell parameters a = 41.5, b = 58.4 and c = 99.3 . Molecular replacement studies indicate that the cucurmosin structure is homologous to trichosanthin. The initial structural model has been obtained and the model fitting/ refinement is in progress.展开更多
A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function...A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function more robust and independent of a specific set of weights for scoring and ranking. The previously described new rotation function calculates the rotation function of molecular replacement by matching the search model directly with the Patterson vector map. The signal-to-noise ratio for the correct match was increased by averaging all the matching peaks. Several matching scores were employed to evaluate the goodness of matching. These matching scores were then combined into a single total score by optimizing a set of weights using the linear regression method. It was found that there exists an optimal set of weights that can be applied to the global rotation search and the correct solution can be ranked in the top 100 or less. However, this set of optimal weights in general is dependent on the search models and the crystal structures with different space groups and cell parameters. In this work, we try to solve this problem by designing a dynamic correlation coefficient. It is shown that the dynamic correlation coefficient works for a variety of space groups and cell parameters in the global search of rotation function. We also introduce two new matching scores： relative entropy and mean-square-residues. Last but not least, we discussed a valid method for the optimization of the adjustable parameters for matching vectors.展开更多
Crotin Ⅱ is one of the ribosome inactivating proteins (RIPs). It belongs to RNA hydrolase. The crystals of crotin Ⅱ are hexagonal with a=b= 94. 62, c=28. 44 A, space group P61, Mr= 14900 Da. The structure was solved...Crotin Ⅱ is one of the ribosome inactivating proteins (RIPs). It belongs to RNA hydrolase. The crystals of crotin Ⅱ are hexagonal with a=b= 94. 62, c=28. 44 A, space group P61, Mr= 14900 Da. The structure was solved by molecularreplacement methed using the molecular structure of RNase T1 as a search model andrefined to R= 0. 25 for the reflections within 10- 2. 5 A resolution range. The refinedmodel cotains one α-helix, one two-strand antiparallel β-sheet and one five-strand an-tiparallel β-sheet. Four conservative residues His47, Glu77, Arg102 and His117 gathering in the cleft of the structure form the possible active site of crotin Ⅱ.展开更多
基金Supported by the National Natural Science Foundation of China (39970872) NSF of Fujian province+1 种基金 and International Cooperation program of Fujian province to the State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Struct
文摘High diffraction quality crystals of cucurmosin, a type I ribosome inactivating protein isolated from the sarcocarp of Cucurbita moschata (pumpkin), have been grown under newly optimised conditions. With in-house rotating anode X-ray source, these crystals diffract to 1.65 ?resolution which is much higher than that of the previously reported crystals that diffracted only to 3 ?resolution. The crystals belong to space group P212121 with cell parameters a = 41.5, b = 58.4 and c = 99.3 . Molecular replacement studies indicate that the cucurmosin structure is homologous to trichosanthin. The initial structural model has been obtained and the model fitting/ refinement is in progress.
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 10674172 and 10874229)
文摘A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function more robust and independent of a specific set of weights for scoring and ranking. The previously described new rotation function calculates the rotation function of molecular replacement by matching the search model directly with the Patterson vector map. The signal-to-noise ratio for the correct match was increased by averaging all the matching peaks. Several matching scores were employed to evaluate the goodness of matching. These matching scores were then combined into a single total score by optimizing a set of weights using the linear regression method. It was found that there exists an optimal set of weights that can be applied to the global rotation search and the correct solution can be ranked in the top 100 or less. However, this set of optimal weights in general is dependent on the search models and the crystal structures with different space groups and cell parameters. In this work, we try to solve this problem by designing a dynamic correlation coefficient. It is shown that the dynamic correlation coefficient works for a variety of space groups and cell parameters in the global search of rotation function. We also introduce two new matching scores： relative entropy and mean-square-residues. Last but not least, we discussed a valid method for the optimization of the adjustable parameters for matching vectors.
文摘Crotin Ⅱ is one of the ribosome inactivating proteins (RIPs). It belongs to RNA hydrolase. The crystals of crotin Ⅱ are hexagonal with a=b= 94. 62, c=28. 44 A, space group P61, Mr= 14900 Da. The structure was solved by molecularreplacement methed using the molecular structure of RNase T1 as a search model andrefined to R= 0. 25 for the reflections within 10- 2. 5 A resolution range. The refinedmodel cotains one α-helix, one two-strand antiparallel β-sheet and one five-strand an-tiparallel β-sheet. Four conservative residues His47, Glu77, Arg102 and His117 gathering in the cleft of the structure form the possible active site of crotin Ⅱ.
