1pfo
PERFRINGOLYSIN O
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 | 1pfo |
| 沉积日期 deposition_date | 1997-07-31 |
| 结构标题 title | PERFRINGOLYSIN O |
| 关键词 keywords | TOXIN, THIOL-ACTIVATED CYTOLYSIN, HEMOLYSIS, CYTOLYSIS; TOXIN |
| 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 | 32.92 Å |
| 回转半径 Rg (电子) rg_electron | 33.48 Å |
| 零角强度 I(0) i0 | 44762000.00 |
| 分子量 molecular_weight | 52506.0 kDa |
| 排除体积 excluded_volume | 65689 ų |
| 包络体积 envelope_volume | 85461 ų |
| 水化壳体积 shell_volume | 24855 ų |
| 包络直径 envelope_diameter | 120.8 Å |
| 壳层 Rg shell_rg | 34.18 Å |
| 包络 Rg envelope_rg | 33.61 Å |
| 形状 Rg shape_rg | 33.53 Å |
| 总 Rg total_rg | 33.38 Å |
| 总原子数 total_atoms | 3705 |
| 残基数 n_residues | 471 |
| 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 | 114.3 Å |
| Rg (实空间) rg_real | 33.64 Å |
| Rg 误差 (实空间) rg_real_error | 1.13 Å |
| I(0) (实空间) i0_real | 4.4760e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.0680e+05 |
| Rg (倒空间) rg_reciprocal | 33.34 Å |
| I(0) (倒空间) i0_reciprocal | 44750000.0000 |
| 解质量估计 total_estimate | 0.7332 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 26.2 Å |
| 偏度 Skewness skewness | 0.674 |
| 峰度 Kurtosis kurtosis | -0.212 |
| 角度范围 angular_range | — – 0.2400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5260000.0000 |
| 实空间数据点数 n_real_points | 49 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.381; Smooth: 0.254 |
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) 6 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1pfoa1 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.69 — Perfringolysin N-terminal-like |
| 超家族 Superfamily superfamily | f.69.1 — Perfringolysin N-terminal-like |
| 家族 Family family | f.69.1.1 — Perfringolysin N-terminal-like |
| 结构域编号 domain_id | d1pfoa2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.183 — Perfringolysin C-terminal-like |
| 超家族 Superfamily superfamily | b.183.1 — Perfringolysin C-terminal-like |
| 家族 Family family | b.183.1.1 — Perfringolysin C-terminal-like |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1pfoA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 840 — HIV-1 Reverse Transcriptase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain |
| 结构域编号 domain_id | 1pfoA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1040 — Carboxypeptidase Inhibitor; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1pfoA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 40 — Perfringolysin |
| 结构域编号 domain_id | 1pfoA04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1430 — Perfringolysin, domain 4 |