1kz7
Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex with the Placental Isoform of Human Cdc42
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 | 1kz7 |
| 沉积日期 deposition_date | 2002-02-06 |
| 结构标题 title | Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex with the Placental Isoform of Human Cdc42 |
| 关键词 keywords | guanine nucleotide exchange factor (GEF), small G-protein, 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 | 36.23 Å |
| 回转半径 Rg (电子) rg_electron | 35.71 Å |
| 零角强度 I(0) i0 | 216952000.00 |
| 分子量 molecular_weight | 118810.0 kDa |
| 排除体积 excluded_volume | 148530 ų |
| 包络体积 envelope_volume | 200360 ų |
| 水化壳体积 shell_volume | 47070 ų |
| 包络直径 envelope_diameter | 122.4 Å |
| 壳层 Rg shell_rg | 42.04 Å |
| 包络 Rg envelope_rg | 34.76 Å |
| 形状 Rg shape_rg | 35.71 Å |
| 总 Rg total_rg | 36.17 Å |
| 总原子数 total_atoms | 8275 |
| 残基数 n_residues | 1012 |
| 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 | 121.4 Å |
| Rg (实空间) rg_real | 36.21 Å |
| Rg 误差 (实空间) rg_real_error | 1.16 Å |
| I(0) (实空间) i0_real | 2.1700e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.3530e+06 |
| Rg (倒空间) rg_reciprocal | 36.22 Å |
| I(0) (倒空间) i0_reciprocal | 217000000.0000 |
| 解质量估计 total_estimate | 0.8901 |
| 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 | 41.4 Å |
| 偏度 Skewness skewness | 0.306 |
| 峰度 Kurtosis kurtosis | -0.390 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 19810000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.925 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1kz7a1 |
| 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 | d1kz7a2 |
| 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 | d1kz7b_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.8 — G proteins |
| 结构域编号 domain_id | d1kz7c1 |
| 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 | d1kz7c2 |
| 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 | d1kz7d_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.8 — G proteins |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1kz7A01 |
| 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 | 1kz7A02 |
| 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 | 1kz7B00 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1kz7C01 |
| 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 | 1kz7C02 |
| 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 | 1kz7D00 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |