8s6h
;Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex ;
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 8s6h |
| 沉积日期 deposition_date | 2024-02-27 |
| 结构标题 title | ;Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex ; |
| 关键词 keywords | ;Conjugal transfer protein, VirB2, Conjugative pilus, Type-4 secretion system fibre, Conduit for horizontal gene transfer, anti-microbial resistance, PROTEIN FIBRIL ;; PROTEIN FIBRIL |
| 实验方法 method | ELECTRON MICROSCOPY |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 62.14 Å |
| 回转半径 Rg (电子) rg_electron | 62.44 Å |
| 零角强度 I(0) i0 | 3213090000.00 |
| 分子量 molecular_weight | 558750.0 kDa |
| 排除体积 excluded_volume | 735010 ų |
| 包络体积 envelope_volume | 976320 ų |
| 水化壳体积 shell_volume | 133330 ų |
| 包络直径 envelope_diameter | 237.1 Å |
| 壳层 Rg shell_rg | 60.74 Å |
| 包络 Rg envelope_rg | 62.74 Å |
| 形状 Rg shape_rg | 62.45 Å |
| 总 Rg total_rg | 62.38 Å |
| 总原子数 total_atoms | 39192 |
| 残基数 n_residues | 4761 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 203.4 Å |
| Rg (实空间) rg_real | 62.56 Å |
| Rg 误差 (实空间) rg_real_error | 1.34 Å |
| I(0) (实空间) i0_real | 3.2110e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.5170e+07 |
| Rg (倒空间) rg_reciprocal | 61.67 Å |
| I(0) (倒空间) i0_reciprocal | 3208000000.0000 |
| 解质量估计 total_estimate | 0.7924 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 65.1 Å |
| 偏度 Skewness skewness | 0.614 |
| 峰度 Kurtosis kurtosis | -0.082 |
| 角度范围 angular_range | — – 0.1250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0022 |
| 最高正则化参数 α highest_alpha | 1673000000.0000 |
| 实空间数据点数 n_real_points | 26 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.690; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.236 |