2b6b
Cryo EM structure of Dengue complexed with CRD of DC-SIGN
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 | 2b6b |
| 沉积日期 deposition_date | 2005-09-30 |
| 结构标题 title | Cryo EM structure of Dengue complexed with CRD of DC-SIGN |
| 关键词 keywords | Cryo EM dengue CRD DC-SIGN, Icosahedral virus, Virus-Receptor COMPLEX; Virus/Receptor |
| 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 | 49.98 Å |
| 回转半径 Rg (电子) rg_electron | 51.13 Å |
| 零角强度 I(0) i0 | 308073000.00 |
| 分子量 molecular_weight | 144710.0 kDa |
| 排除体积 excluded_volume | 176750 ų |
| 包络体积 envelope_volume | 178350 ų |
| 水化壳体积 shell_volume | 34095 ų |
| 包络直径 envelope_diameter | 188.1 Å |
| 壳层 Rg shell_rg | 44.99 Å |
| 包络 Rg envelope_rg | 48.87 Å |
| 形状 Rg shape_rg | 51.26 Å |
| 总 Rg total_rg | 50.93 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 | 178.5 Å |
| Rg (实空间) rg_real | 50.77 Å |
| Rg 误差 (实空间) rg_real_error | 2.07 Å |
| I(0) (实空间) i0_real | 3.0810e+08 |
| I(0) 误差 (实空间) i0_real_error | 5.7810e+06 |
| Rg (倒空间) rg_reciprocal | 49.99 Å |
| I(0) (倒空间) i0_reciprocal | 307700000.0000 |
| 解质量估计 total_estimate | 0.8233 |
| 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 | 61.4 Å |
| 偏度 Skewness skewness | 0.584 |
| 峰度 Kurtosis kurtosis | 0.004 |
| 角度范围 angular_range | — – 0.1600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11580000.0000 |
| 实空间数据点数 n_real_points | 33 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.779; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.596 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (7 domains)
| 结构域编号 domain_id | d2b6ba1 |
| 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 | d2b6ba2 |
| 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 | d2b6bb1 |
| 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 | d2b6bb2 |
| 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 | d2b6bc1 |
| 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 | d2b6bc2 |
| 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 | d2b6bd1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.169 — C-type lectin-like |
| 超家族 Superfamily superfamily | d.169.1 — C-type lectin-like |
| 家族 Family family | d.169.1.1 — C-type lectin domain |