1xf1
Structure of C5a peptidase- a key virulence factor from Streptococcus
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 | 1xf1 |
| 沉积日期 deposition_date | 2004-09-13 |
| 结构标题 title | Structure of C5a peptidase- a key virulence factor from Streptococcus |
| 关键词 keywords | C5a peptidase, hydrolase; HYDROLASE |
| 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 | 45.25 Å |
| 回转半径 Rg (电子) rg_electron | 45.50 Å |
| 零角强度 I(0) i0 | 659043000.00 |
| 分子量 molecular_weight | 206550.0 kDa |
| 排除体积 excluded_volume | 255670 ų |
| 包络体积 envelope_volume | 343690 ų |
| 水化壳体积 shell_volume | 64809 ų |
| 包络直径 envelope_diameter | 159.6 Å |
| 壳层 Rg shell_rg | 48.36 Å |
| 包络 Rg envelope_rg | 44.48 Å |
| 形状 Rg shape_rg | 45.42 Å |
| 总 Rg total_rg | 45.89 Å |
| 总原子数 total_atoms | 14452 |
| 残基数 n_residues | 1820 |
| 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 | 156.0 Å |
| Rg (实空间) rg_real | 45.51 Å |
| Rg 误差 (实空间) rg_real_error | 2.10 Å |
| I(0) (实空间) i0_real | 6.5900e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1870e+07 |
| Rg (倒空间) rg_reciprocal | 45.25 Å |
| I(0) (倒空间) i0_reciprocal | 658800000.0000 |
| 解质量估计 total_estimate | 0.8472 |
| 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 | 44.6 Å |
| 偏度 Skewness skewness | 0.468 |
| 峰度 Kurtosis kurtosis | -0.397 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 66010000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.784; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.776 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 8 domains
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1xf1A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 200 — Peptidase S8/S53 domain |
| 结构域编号 domain_id | 1xf1A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 30 — Glucose Oxidase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1xf1A03 |
| 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 | 1710 — Subtilisin-like superfamily |
| 结构域编号 domain_id | 1xf1A05 |
| 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 | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1xf1B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 200 — Peptidase S8/S53 domain |
| 结构域编号 domain_id | 1xf1B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 30 — Glucose Oxidase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1xf1B03 |
| 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 | 1710 — Subtilisin-like superfamily |
| 结构域编号 domain_id | 1xf1B05 |
| 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 | 10 — Immunoglobulins |