1t5r
STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS
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 | 1t5r |
| 沉积日期 deposition_date | 2004-05-05 |
| 结构标题 title | STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN S COMPONENT FROM STAPHYLOCOCCUS AUREUS |
| 关键词 keywords | BI-COMPONENT LEUCOTOXIN, PORE-FORMING TOXIN, STAPHYLOCOCCUS AUREUS, S COMPONENT LEUCOCIDIN, UNKNOWN FUNCTION; UNKNOWN FUNCTION |
| 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 | 50.58 Å |
| 回转半径 Rg (电子) rg_electron | 50.41 Å |
| 零角强度 I(0) i0 | 889592000.00 |
| 分子量 molecular_weight | 241220.0 kDa |
| 排除体积 excluded_volume | 298460 ų |
| 包络体积 envelope_volume | 440100 ų |
| 水化壳体积 shell_volume | 73810 ų |
| 包络直径 envelope_diameter | 177.4 Å |
| 壳层 Rg shell_rg | 52.74 Å |
| 包络 Rg envelope_rg | 49.21 Å |
| 形状 Rg shape_rg | 50.41 Å |
| 总 Rg total_rg | 50.49 Å |
| 总原子数 total_atoms | 17092 |
| 残基数 n_residues | 2151 |
| 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 | 170.0 Å |
| Rg (实空间) rg_real | 50.63 Å |
| Rg 误差 (实空间) rg_real_error | 1.51 Å |
| I(0) (实空间) i0_real | 8.8960e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.6240e+07 |
| Rg (倒空间) rg_reciprocal | 50.52 Å |
| I(0) (倒空间) i0_reciprocal | 889400000.0000 |
| 解质量估计 total_estimate | 0.8783 |
| 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 | 54.8 Å |
| 偏度 Skewness skewness | 0.344 |
| 峰度 Kurtosis kurtosis | -0.468 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 49800000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.810 |
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) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1t5ra_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5rb_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5rc_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5rd_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5re_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5rf_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5rg_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
| 结构域编号 domain_id | d1t5rh_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.6 — Leukocidin-like |
| 超家族 Superfamily superfamily | f.6.1 — Leukocidin-like |
| 家族 Family family | f.6.1.1 — Leukocidin (pore-forming toxin) |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1t5rA00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rB00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rC00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rD00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rE00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rF00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rG00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |
| 结构域编号 domain_id | 1t5rH00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 240 — Leukocidin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leukocidin/porin MspA |