1xd4
Crystal structure of the DH-PH-cat module of Son of Sevenless (SOS)
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 | 1xd4 |
| 沉积日期 deposition_date | 2004-09-03 |
| 结构标题 title | Crystal structure of the DH-PH-cat module of Son of Sevenless (SOS) |
| 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 | 58.86 Å |
| 回转半径 Rg (电子) rg_electron | 59.94 Å |
| 零角强度 I(0) i0 | 522263000.00 |
| 分子量 molecular_weight | 192210.0 kDa |
| 排除体积 excluded_volume | 242000 ų |
| 包络体积 envelope_volume | 399030 ų |
| 水化壳体积 shell_volume | 62328 ų |
| 包络直径 envelope_diameter | 219.9 Å |
| 壳层 Rg shell_rg | 50.20 Å |
| 包络 Rg envelope_rg | 60.02 Å |
| 形状 Rg shape_rg | 59.90 Å |
| 总 Rg total_rg | 59.72 Å |
| 总原子数 total_atoms | 13542 |
| 残基数 n_residues | 1648 |
| 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 | 197.0 Å |
| Rg (实空间) rg_real | 59.93 Å |
| Rg 误差 (实空间) rg_real_error | 2.37 Å |
| I(0) (实空间) i0_real | 5.2220e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1020e+07 |
| Rg (倒空间) rg_reciprocal | 57.94 Å |
| I(0) (倒空间) i0_reciprocal | 520600000.0000 |
| 解质量估计 total_estimate | 0.7564 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 43.8 Å |
| 偏度 Skewness skewness | 0.682 |
| 峰度 Kurtosis kurtosis | -0.118 |
| 角度范围 angular_range | — – 0.1350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 24370000.0000 |
| 实空间数据点数 n_real_points | 28 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.725; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.594; Smooth: 0.061 |
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) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1xd4a1 |
| 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 | d1xd4a2 |
| 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 | d1xd4a3 |
| 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 | d1xd4b1 |
| 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 | d1xd4b2 |
| 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 | d1xd4b3 |
| 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) |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1xd4A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 900 — Dbl Homology Domain; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dbl homology (DH) domain |
| 结构域编号 domain_id | 1xd4A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 29 — PH-domain like |
| 同源超家族 H-superfamily homologous superfamily | 30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) |
| 结构域编号 domain_id | 1xd4A03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 870 — Son of sevenless (SoS) protein; Chain S, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Son of sevenless (SoS) protein Chain: S domain 1 |
| 结构域编号 domain_id | 1xd4A04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 840 — Son of Sevenless (SoS) protein; Chain S, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ras guanine-nucleotide exchange factors catalytic domain |
| 结构域编号 domain_id | 1xd4B01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 900 — Dbl Homology Domain; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dbl homology (DH) domain |
| 结构域编号 domain_id | 1xd4B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 29 — PH-domain like |
| 同源超家族 H-superfamily homologous superfamily | 30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) |
| 结构域编号 domain_id | 1xd4B03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 870 — Son of sevenless (SoS) protein; Chain S, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Son of sevenless (SoS) protein Chain: S domain 1 |
| 结构域编号 domain_id | 1xd4B04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 840 — Son of Sevenless (SoS) protein; Chain S, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ras guanine-nucleotide exchange factors catalytic domain |