1xdv
Experimentally Phased Structure of Human the Son of Sevenless protein at 4.1 Ang.
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 | 1xdv |
| 沉积日期 deposition_date | 2004-09-08 |
| 结构标题 title | Experimentally Phased Structure of Human the Son of Sevenless protein at 4.1 Ang. |
| 关键词 keywords | nucleotide exchange factor, Ras, Cdc25, Ras exchanger motif (Rem), Dbl homology(DH), pleckstrin homology (PH), SIGNALING PROTEIN; SIGNALING 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 | 57.04 Å |
| 回转半径 Rg (电子) rg_electron | 58.37 Å |
| 零角强度 I(0) i0 | 441020000.00 |
| 分子量 molecular_weight | 177550.0 kDa |
| 排除体积 excluded_volume | 224150 ų |
| 包络体积 envelope_volume | 346670 ų |
| 水化壳体积 shell_volume | 57571 ų |
| 包络直径 envelope_diameter | 221.7 Å |
| 壳层 Rg shell_rg | 47.69 Å |
| 包络 Rg envelope_rg | 58.37 Å |
| 形状 Rg shape_rg | 58.33 Å |
| 总 Rg total_rg | 58.06 Å |
| 总原子数 total_atoms | 12516 |
| 残基数 n_residues | 1517 |
| 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 | 160.9 Å |
| Rg (实空间) rg_real | 52.99 Å |
| Rg 误差 (实空间) rg_real_error | 0.86 Å |
| I(0) (实空间) i0_real | 4.2500e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.0480e+06 |
| Rg (倒空间) rg_reciprocal | 56.11 Å |
| I(0) (倒空间) i0_reciprocal | 439700000.0000 |
| 解质量估计 total_estimate | 0.7205 |
| 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 | 40.2 Å |
| 偏度 Skewness skewness | 0.446 |
| 峰度 Kurtosis kurtosis | -0.490 |
| 角度范围 angular_range | — – 0.1400 Å−1 |
| 当前正则化参数 α current_alpha | 0.1144 |
| 最高正则化参数 α highest_alpha | 15350000.0000 |
| 实空间数据点数 n_real_points | 29 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.001; Oscil: 0.921; Stabil: 0.966; Sysdev: 0.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.815 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1xdva1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.87 — DBL homology domain (DH-domain) |
| 超家族 Superfamily superfamily | a.87.1 — DBL homology domain (DH-domain) |
| 家族 Family family | a.87.1.1 — DBL homology domain (DH-domain) |
| 结构域编号 domain_id | d1xdva2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.117 — Ras GEF |
| 超家族 Superfamily superfamily | a.117.1 — Ras GEF |
| 家族 Family family | a.117.1.1 — Ras GEF |
| 结构域编号 domain_id | d1xdva3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.55 — PH domain-like barrel |
| 超家族 Superfamily superfamily | b.55.1 — PH domain-like |
| 家族 Family family | b.55.1.1 — Pleckstrin-homology domain (PH domain) |
| 结构域编号 domain_id | d1xdvb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.87 — DBL homology domain (DH-domain) |
| 超家族 Superfamily superfamily | a.87.1 — DBL homology domain (DH-domain) |
| 家族 Family family | a.87.1.1 — DBL homology domain (DH-domain) |
| 结构域编号 domain_id | d1xdvb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.117 — Ras GEF |
| 超家族 Superfamily superfamily | a.117.1 — Ras GEF |
| 家族 Family family | a.117.1.1 — Ras GEF |
| 结构域编号 domain_id | d1xdvb3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.55 — PH domain-like barrel |
| 超家族 Superfamily superfamily | b.55.1 — PH domain-like |
| 家族 Family family | b.55.1.1 — Pleckstrin-homology domain (PH domain) |