Supplementary Data for: "Molecular basis for bacterial N-glycosylation by a soluble HMW1C-like N-glycosyltransferase"

This data set contains files related to the article "<strong>Molecular basis for bacterial <em>N</em>-glycosylation by a soluble HMW1C-like <em>N</em>-glycosyltransferase</strong>" by Beatriz Piniello, Javier Macías-León, Shun Miyazaki, Ana García-García, Ismael Compañón, Mattia Ghirardello, Víctor Taleb, Billy Veloz, Francisco Corzana, Atsushi Miyagawa, Carme Rovira and Ramón Hurtado-Guerrero. Description of the files: <strong>Simulation data:</strong> - <strong>classical_md_simulations.zip: </strong>includes the inputs and initial and final structures of the classical MD simulation of AaNGT in complex with UDP-Glc and peptide, for both Asn3 in amide and imidic acid form. - <strong>qmmm_simulations.zip</strong>: includes the inputs for equilibration and metadynamics, and the initial structure extracted from the classical MD. Other relevant structures included in the directories of the pertinent figures (see below). Also includes plots of the CVs for each of the metadynamics. <strong>Data related to the figures in the manuscript (data from the plots is in the Source Data file included with the manuscript):</strong> <strong>- Figure_4.zip: </strong>PDB file of the structure shown. - <strong>Figure_5.zip</strong>: PDB files of the structures shown (MC, TS and P, (already uploaded in v1) and FES file. - <strong>Figure_S6.zip: </strong>PDB files of the structures shown (MC, TS and P). - <strong>Figure_S7.zip: </strong>PDB files of the structures shown (MC, TS and P) for both simulations, and their respective FES files. - <strong>Figure_S9.zip</strong>: PDB file of the structure shown (computational only). It is the same as the structure shown in <strong>Figure 8</strong>. - <strong>Figure_S11.zip</strong>: PDB file of the structure shown. - <strong>Table_S3.zip: </strong>Excel file with the data to obtain the table. TS is given as a single structure in the table and thus not included in the file. More data can be made available upon reasonable request.本数据集包含Beatriz Piniello、Javier Macías-León、Shun Miyazaki、Ana García-García、Ismael Compañón、Mattia Ghirardello、Víctor Taleb、Billy Veloz、Francisco Corzana、Atsushi Miyagawa、Carme Rovira及Ramón Hurtado-Guerrero联合发表的论文《可溶性类HMW1C型N-糖基转移酶介导细菌N-糖基化的分子机制》相关文件。 文件说明如下： **模拟数据：** - **classical_md_simulations.zip**：包含AaNGT与UDP-Glc（尿苷二磷酸葡萄糖）、肽段形成复合物的经典分子动力学（Classical Molecular Dynamics, MD）模拟的输入文件、初始结构与最终结构，覆盖酰胺态与亚胺酸态两种形式的Asn3位点。 - **qmmm_simulations.zip**：包含平衡化模拟与元动力学（Metadynamics）的输入文件，以及从经典MD模拟中提取的初始结构。相关配图目录中收录了其他必要结构（详见下文），此外还包含各次元动力学模拟的集体变量（Collective Variables, CVs）变化曲线。 **论文配图相关数据（绘图原始数据收录于论文附带的源数据文件）：** - **Figure_4.zip**：对应正文中图4展示结构的蛋白质数据银行（Protein Data Bank, PDB）格式文件。 - **Figure_5.zip**：包含正文中图5展示的MC、TS、P三种结构的PDB格式文件（该内容已在v1版本上传），以及自由能面（Free Energy Surface, FES）文件。 - **Figure_S6.zip**：包含补充图S6展示的MC、TS、P三种结构的PDB格式文件。 - **Figure_S7.zip**：包含两次模拟对应的MC、TS、P三种结构的PDB格式文件，以及各自对应的自由能面文件。 - **Figure_S9.zip**：对应补充图S9展示的仅用于计算的结构的PDB格式文件，该结构与正文中图8展示的结构一致。 - **Figure_S11.zip**：对应补充图S11展示结构的PDB格式文件。 - **Table_S3.zip**：包含用于生成附表S3的Excel格式数据文件。附表S3中将TS以单一结构形式给出，因此该压缩包中未包含TS相关数据。如有合理需求，可另行提供更多数据。