1thd
COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION
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 | 1thd |
| 沉积日期 deposition_date | 2004-06-01 |
| 结构标题 title | COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION |
| 关键词 keywords | FLAVIVIRUS, FLAVIVIRIDAE, DENGUE VIRUS, GLYCOPROTEIN E, CRYO-EM, Icosahedral virus, Virus; VIRUS |
| 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 | 51.28 Å |
| 回转半径 Rg (电子) rg_electron | 52.24 Å |
| 零角强度 I(0) i0 | 247238000.00 |
| 分子量 molecular_weight | 130050.0 kDa |
| 排除体积 excluded_volume | 159190 ų |
| 包络体积 envelope_volume | 164570 ų |
| 水化壳体积 shell_volume | 31347 ų |
| 包络直径 envelope_diameter | 191.9 Å |
| 壳层 Rg shell_rg | 44.72 Å |
| 包络 Rg envelope_rg | 50.09 Å |
| 形状 Rg shape_rg | 52.34 Å |
| 总 Rg total_rg | 52.00 Å |
| 总原子数 total_atoms | — |
| 残基数 n_residues | — |
| 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 | 180.7 Å |
| Rg (实空间) rg_real | 51.91 Å |
| Rg 误差 (实空间) rg_real_error | 1.80 Å |
| I(0) (实空间) i0_real | 2.4720e+08 |
| I(0) 误差 (实空间) i0_real_error | 5.2610e+06 |
| Rg (倒空间) rg_reciprocal | 50.76 Å |
| I(0) (倒空间) i0_reciprocal | 246800000.0000 |
| 解质量估计 total_estimate | 0.7740 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 40.8 Å |
| 偏度 Skewness skewness | 0.622 |
| 峰度 Kurtosis kurtosis | -0.179 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0019 |
| 最高正则化参数 α highest_alpha | 8118000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.707; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.468; Smooth: 0.470 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1thda1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.4 — Class II viral fusion proteins C-terminal domain |
| 结构域编号 domain_id | d1thda2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.10 — Viral glycoprotein, central and dimerisation domains |
| 超家族 Superfamily superfamily | f.10.1 — Viral glycoprotein, central and dimerisation domains |
| 家族 Family family | f.10.1.1 — Viral glycoprotein, central and dimerisation domains |
| 结构域编号 domain_id | d1thdb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.4 — Class II viral fusion proteins C-terminal domain |
| 结构域编号 domain_id | d1thdb2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.10 — Viral glycoprotein, central and dimerisation domains |
| 超家族 Superfamily superfamily | f.10.1 — Viral glycoprotein, central and dimerisation domains |
| 家族 Family family | f.10.1.1 — Viral glycoprotein, central and dimerisation domains |
| 结构域编号 domain_id | d1thdc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.4 — Class II viral fusion proteins C-terminal domain |
| 结构域编号 domain_id | d1thdc2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.10 — Viral glycoprotein, central and dimerisation domains |
| 超家族 Superfamily superfamily | f.10.1 — Viral glycoprotein, central and dimerisation domains |
| 家族 Family family | f.10.1.1 — Viral glycoprotein, central and dimerisation domains |