1slq
Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT
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 | 1slq |
| 沉积日期 deposition_date | 2004-03-06 |
| 结构标题 title | Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT |
| 关键词 keywords | ;beta sandwich, greek key, alpha helical triple coiled-coil, membrane penetration protein, non-enveloped virus, spike protein, 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 | 43.28 Å |
| 回转半径 Rg (电子) rg_electron | 43.12 Å |
| 零角强度 I(0) i0 | 489764000.00 |
| 分子量 molecular_weight | 180890.0 kDa |
| 排除体积 excluded_volume | 225790 ų |
| 包络体积 envelope_volume | 312100 ų |
| 水化壳体积 shell_volume | 61639 ų |
| 包络直径 envelope_diameter | 143.0 Å |
| 壳层 Rg shell_rg | 47.37 Å |
| 包络 Rg envelope_rg | 41.62 Å |
| 形状 Rg shape_rg | 43.09 Å |
| 总 Rg total_rg | 43.40 Å |
| 总原子数 total_atoms | 12772 |
| 残基数 n_residues | 1604 |
| 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 | 143.0 Å |
| Rg (实空间) rg_real | 43.38 Å |
| Rg 误差 (实空间) rg_real_error | 1.57 Å |
| I(0) (实空间) i0_real | 4.8980e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.1690e+06 |
| Rg (倒空间) rg_reciprocal | 43.28 Å |
| I(0) (倒空间) i0_reciprocal | 489700000.0000 |
| 解质量估计 total_estimate | 0.8690 |
| 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 | 43.7 Å |
| 偏度 Skewness skewness | 0.372 |
| 峰度 Kurtosis kurtosis | -0.501 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 41460000.0000 |
| 实空间数据点数 n_real_points | 37 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.678 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1slqa_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.47 — VP4 membrane interaction domain |
| 超家族 Superfamily superfamily | f.47.1 — VP4 membrane interaction domain |
| 家族 Family family | f.47.1.1 — VP4 membrane interaction domain |
| 结构域编号 domain_id | d1slqb_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.47 — VP4 membrane interaction domain |
| 超家族 Superfamily superfamily | f.47.1 — VP4 membrane interaction domain |
| 家族 Family family | f.47.1.1 — VP4 membrane interaction domain |
| 结构域编号 domain_id | d1slqc_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.47 — VP4 membrane interaction domain |
| 超家族 Superfamily superfamily | f.47.1 — VP4 membrane interaction domain |
| 家族 Family family | f.47.1.1 — VP4 membrane interaction domain |
| 结构域编号 domain_id | d1slqd_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.47 — VP4 membrane interaction domain |
| 超家族 Superfamily superfamily | f.47.1 — VP4 membrane interaction domain |
| 家族 Family family | f.47.1.1 — VP4 membrane interaction domain |
| 结构域编号 domain_id | d1slqe_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.47 — VP4 membrane interaction domain |
| 超家族 Superfamily superfamily | f.47.1 — VP4 membrane interaction domain |
| 家族 Family family | f.47.1.1 — VP4 membrane interaction domain |
| 结构域编号 domain_id | d1slqf_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.47 — VP4 membrane interaction domain |
| 超家族 Superfamily superfamily | f.47.1 — VP4 membrane interaction domain |
| 家族 Family family | f.47.1.1 — VP4 membrane interaction domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1slqA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1slqB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1slqC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1slqD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1slqE02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1slqF02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |