1td0
Viral capsid protein SHP at pH 5.5
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 | 1td0 |
| 沉积日期 deposition_date | 2004-05-21 |
| 结构标题 title | Viral capsid protein SHP at pH 5.5 |
| 关键词 keywords | SHP, 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 | 31.81 Å |
| 回转半径 Rg (电子) rg_electron | 32.03 Å |
| 零角强度 I(0) i0 | 27535600.00 |
| 分子量 molecular_weight | 41157.0 kDa |
| 排除体积 excluded_volume | 51511 ų |
| 包络体积 envelope_volume | 68929 ų |
| 水化壳体积 shell_volume | 20489 ų |
| 包络直径 envelope_diameter | 111.5 Å |
| 壳层 Rg shell_rg | 33.81 Å |
| 包络 Rg envelope_rg | 32.08 Å |
| 形状 Rg shape_rg | 32.01 Å |
| 总 Rg total_rg | 32.26 Å |
| 总原子数 total_atoms | 2911 |
| 残基数 n_residues | 408 |
| 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 | 111.8 Å |
| Rg (实空间) rg_real | 32.43 Å |
| Rg 误差 (实空间) rg_real_error | 1.13 Å |
| I(0) (实空间) i0_real | 2.7540e+07 |
| I(0) 误差 (实空间) i0_real_error | 4.5910e+05 |
| Rg (倒空间) rg_reciprocal | 32.17 Å |
| I(0) (倒空间) i0_reciprocal | 27530000.0000 |
| 解质量估计 total_estimate | 0.5200 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 22.4 Å |
| 偏度 Skewness skewness | 0.579 |
| 峰度 Kurtosis kurtosis | -0.518 |
| 角度范围 angular_range | — – 0.2500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 4687000.0000 |
| 实空间数据点数 n_real_points | 51 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.427; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.271; Smooth: 0.699 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1td0a_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.85 — beta-clip |
| 超家族 Superfamily superfamily | b.85.2 — Head decoration protein D (gpD, major capsid protein D) |
| 家族 Family family | b.85.2.1 — Head decoration protein D (gpD, major capsid protein D) |
| 结构域编号 domain_id | d1td0b_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.85 — beta-clip |
| 超家族 Superfamily superfamily | b.85.2 — Head decoration protein D (gpD, major capsid protein D) |
| 家族 Family family | b.85.2.1 — Head decoration protein D (gpD, major capsid protein D) |
| 结构域编号 domain_id | d1td0c_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.85 — beta-clip |
| 超家族 Superfamily superfamily | b.85.2 — Head decoration protein D (gpD, major capsid protein D) |
| 家族 Family family | b.85.2.1 — Head decoration protein D (gpD, major capsid protein D) |
| 结构域编号 domain_id | d1td0d_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.85 — beta-clip |
| 超家族 Superfamily superfamily | b.85.2 — Head decoration protein D (gpD, major capsid protein D) |
| 家族 Family family | b.85.2.1 — Head decoration protein D (gpD, major capsid protein D) |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1td0A00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 300 — Virus Head Decoration Protein; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 10 — Head decoration protein D |
| 结构域编号 domain_id | 1td0B00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 300 — Virus Head Decoration Protein; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 10 — Head decoration protein D |
| 结构域编号 domain_id | 1td0C00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 300 — Virus Head Decoration Protein; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 10 — Head decoration protein D |
| 结构域编号 domain_id | 1td0D00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 300 — Virus Head Decoration Protein; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 10 — Head decoration protein D |