Dataset of detected, built and improved tryptophan mannosylation in glycoprotein structures

Dataset corresponding to the work described in paper "Methods for detecting, building and improving tryptophan mannosylation in glycoprotein structures", Holland L., Pham T.P. et al Protein Science Tools (2024). Included are pdb and mmcif files constaining the structures where we modelled unmodelled C-mannosylation (named pdbcode_grafted.pdb/mmcif), pdb and mmcif files containing the structures where we fixed distorted or incorrect C-mannose residues (named pdbcode_fixed.pdb/mmcif), and the mtz files for the X-ray crystal structures. Also included are restraint files for the glycans, to be used with servalcat/refmac5 in order to preserve the glycan conformation and linkage when refining. These files are sorted into folders for X-ray crystal structures and for Cryo-EM structures. Finally, the code used to produce these results (privateer) is included in the version it was when the data was collected.本数据集对应发表于《Protein Science Tools》2024年的论文《Methods for detecting, building and improving tryptophan mannosylation in glycoprotein structures》，作者为Holland L.、Pham T.P.等研究者。数据集包含以下文件：其一为包含我们对未建模C-甘露糖基化位点完成建模的结构的PDB（Protein Data Bank）与mmCIF（macromolecular Crystallographic Information File）文件，命名格式为pdbcode_grafted.pdb/mmcif；其二为包含我们已修正畸变或错误C-甘露糖残基的结构的PDB与mmCIF文件，命名格式为pdbcode_fixed.pdb/mmcif。此外还包含X射线晶体结构对应的MTZ文件。同时附带糖链的约束精修文件，可与servalcat/refmac5软件联用，用于晶体精修过程中维持糖链构象与糖苷键连接方式。上述文件按照X射线晶体结构与冷冻电镜（Cryo-Electron Microscopy, Cryo-EM）结构分为两个专属文件夹存储。此外还附带了用于生成本次数据集结果的代码工具privateer，其版本为数据采集时的官方版本。