1o75
Tp47, the 47-Kilodalton Lipoprotein of Treponema pallidum
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 | 1o75 |
| 沉积日期 deposition_date | 2002-10-23 |
| 结构标题 title | Tp47, the 47-Kilodalton Lipoprotein of Treponema pallidum |
| 关键词 keywords | ;LIPOPROTEINULLNTIGEN, PENICILLIN-BINDING PROTEIN, INTEGRAL MEMBRANE LIPOPROTEIN, IMMUNOGEN, FOUR-DOMAIN PROTEIN, ANTIGEN, LIPOPROTEIN ;; LIPOPROTEINULLNTIGEN |
| 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 | 29.54 Å |
| 回转半径 Rg (电子) rg_electron | 28.93 Å |
| 零角强度 I(0) i0 | 139031000.00 |
| 分子量 molecular_weight | 89745.0 kDa |
| 排除体积 excluded_volume | 110570 ų |
| 包络体积 envelope_volume | 140740 ų |
| 水化壳体积 shell_volume | 40390 ų |
| 包络直径 envelope_diameter | 99.8 Å |
| 壳层 Rg shell_rg | 36.41 Å |
| 包络 Rg envelope_rg | 28.57 Å |
| 形状 Rg shape_rg | 28.92 Å |
| 总 Rg total_rg | 29.63 Å |
| 总原子数 total_atoms | 6281 |
| 残基数 n_residues | 801 |
| 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 | 94.1 Å |
| Rg (实空间) rg_real | 29.43 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 1.3900e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.0560e+06 |
| Rg (倒空间) rg_reciprocal | 29.48 Å |
| I(0) (倒空间) i0_reciprocal | 139000000.0000 |
| 解质量估计 total_estimate | 0.8977 |
| 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 | 36.6 Å |
| 偏度 Skewness skewness | 0.235 |
| 峰度 Kurtosis kurtosis | -0.388 |
| 角度范围 angular_range | — – 0.2700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 26520000.0000 |
| 实空间数据点数 n_real_points | 55 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.966 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1o75a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.20 — Tp47 lipoprotein, middle and C-terminal domains |
| 家族 Family family | b.1.20.1 — Tp47 lipoprotein, middle and C-terminal domains |
| 结构域编号 domain_id | d1o75a2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.20 — Tp47 lipoprotein, middle and C-terminal domains |
| 家族 Family family | b.1.20.1 — Tp47 lipoprotein, middle and C-terminal domains |
| 结构域编号 domain_id | d1o75a3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.120 — Tp47 lipoprotein, N-terminal domain |
| 超家族 Superfamily superfamily | b.120.1 — Tp47 lipoprotein, N-terminal domain |
| 家族 Family family | b.120.1.1 — Tp47 lipoprotein, N-terminal domain |
| 结构域编号 domain_id | d1o75b1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.20 — Tp47 lipoprotein, middle and C-terminal domains |
| 家族 Family family | b.1.20.1 — Tp47 lipoprotein, middle and C-terminal domains |
| 结构域编号 domain_id | d1o75b2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.20 — Tp47 lipoprotein, middle and C-terminal domains |
| 家族 Family family | b.1.20.1 — Tp47 lipoprotein, middle and C-terminal domains |
| 结构域编号 domain_id | d1o75b3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.120 — Tp47 lipoprotein, N-terminal domain |
| 超家族 Superfamily superfamily | b.120.1 — Tp47 lipoprotein, N-terminal domain |
| 家族 Family family | b.120.1.1 — Tp47 lipoprotein, N-terminal domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1o75A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 200 — Penicillin-binding protein Tp47, domain A |
| 结构域编号 domain_id | 1o75A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 470 — Penicillin-binding protein Tp47, domain B |
| 结构域编号 domain_id | 1o75A03 |
| 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 | 1300 — Penicillin-binding protein Tp47, domain C |
| 结构域编号 domain_id | 1o75A04 |
| 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 | 1270 — Penicillin-binding protein Tp47, domain D |
| 结构域编号 domain_id | 1o75B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 200 — Penicillin-binding protein Tp47, domain A |
| 结构域编号 domain_id | 1o75B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 470 — Penicillin-binding protein Tp47, domain B |
| 结构域编号 domain_id | 1o75B03 |
| 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 | 1300 — Penicillin-binding protein Tp47, domain C |
| 结构域编号 domain_id | 1o75B04 |
| 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 | 1270 — Penicillin-binding protein Tp47, domain D |