1yu4
Major Tropism Determinant U1 Variant
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 | 1yu4 |
| 沉积日期 deposition_date | 2005-02-11 |
| 结构标题 title | Major Tropism Determinant U1 Variant |
| 关键词 keywords | C-type Lectin, Beta Sandwich, Beta Prism, variability, diversity-generating retroelement, Viral protein; VIRAL PROTEIN |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 30.79 Å |
| 回转半径 Rg (电子) rg_electron | 29.67 Å |
| 零角强度 I(0) i0 | 232155000.00 |
| 分子量 molecular_weight | 116710.0 kDa |
| 排除体积 excluded_volume | 143800 ų |
| 包络体积 envelope_volume | 170870 ų |
| 水化壳体积 shell_volume | 46260 ų |
| 包络直径 envelope_diameter | 97.7 Å |
| 壳层 Rg shell_rg | 37.97 Å |
| 包络 Rg envelope_rg | 29.66 Å |
| 形状 Rg shape_rg | 29.65 Å |
| 总 Rg total_rg | 30.39 Å |
| 总原子数 total_atoms | 8243 |
| 残基数 n_residues | 1128 |
| 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 | 95.1 Å |
| Rg (实空间) rg_real | 30.63 Å |
| Rg 误差 (实空间) rg_real_error | 0.57 Å |
| I(0) (实空间) i0_real | 2.3220e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.1670e+06 |
| Rg (倒空间) rg_reciprocal | 30.70 Å |
| I(0) (倒空间) i0_reciprocal | 232200000.0000 |
| 解质量估计 total_estimate | 0.9024 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 39.2 Å |
| 偏度 Skewness skewness | 0.173 |
| 峰度 Kurtosis kurtosis | -0.467 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 53960000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.935 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 15 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1yu4a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.163 — Pseudo beta-prism I |
| 超家族 Superfamily superfamily | b.163.1 — Bacteriophage trimeric proteins domain |
| 家族 Family family | b.163.1.1 — Mtd domain-like |
| 结构域编号 domain_id | d1yu4a2 |
| 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.169.1.8 — Mtd variable domain |
| 结构域编号 domain_id | d1yu4b1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.163 — Pseudo beta-prism I |
| 超家族 Superfamily superfamily | b.163.1 — Bacteriophage trimeric proteins domain |
| 家族 Family family | b.163.1.1 — Mtd domain-like |
| 结构域编号 domain_id | d1yu4b2 |
| 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.169.1.8 — Mtd variable domain |
| 结构域编号 domain_id | d1yu4c1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.163 — Pseudo beta-prism I |
| 超家族 Superfamily superfamily | b.163.1 — Bacteriophage trimeric proteins domain |
| 家族 Family family | b.163.1.1 — Mtd domain-like |
| 结构域编号 domain_id | d1yu4c2 |
| 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.169.1.8 — Mtd variable domain |
CATH v4.4 (9 domains)
| 结构域编号 domain_id | 1yu4A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1yu4A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 80 — Trefoil |
| 拓扑 Topology topology | 20 — Tail fiber receptor-binding protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tail fiber receptor-binding protein |
| 结构域编号 domain_id | 1yu4A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1580 — paralog of FGE (formylglycine-generating enzyme) |
| 同源超家族 H-superfamily homologous superfamily | 10 — paralog of FGE (formylglycine-generating enzyme) |
| 结构域编号 domain_id | 1yu4B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1yu4B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 80 — Trefoil |
| 拓扑 Topology topology | 20 — Tail fiber receptor-binding protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tail fiber receptor-binding protein |
| 结构域编号 domain_id | 1yu4B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1580 — paralog of FGE (formylglycine-generating enzyme) |
| 同源超家族 H-superfamily homologous superfamily | 10 — paralog of FGE (formylglycine-generating enzyme) |
| 结构域编号 domain_id | 1yu4C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1yu4C02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 80 — Trefoil |
| 拓扑 Topology topology | 20 — Tail fiber receptor-binding protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tail fiber receptor-binding protein |
| 结构域编号 domain_id | 1yu4C03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1580 — paralog of FGE (formylglycine-generating enzyme) |
| 同源超家族 H-superfamily homologous superfamily | 10 — paralog of FGE (formylglycine-generating enzyme) |