2knb
Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain
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 | 2knb |
| 沉积日期 deposition_date | 2009-08-20 |
| 结构标题 title | Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain |
| 关键词 keywords | ;Ubl, SH3, parkin, endophilin, Cell junction, Cell membrane, Cell projection, Endoplasmic reticulum, Ligase, Membrane, Metal-binding, Nucleus, Postsynaptic cell membrane, S-nitrosylation, Synapse, Ubl conjugation pathway, Zinc-finger, Endocytosis, Lipid-binding, Phosphoprotein, SH3 domain, PROTEIN BINDING ;; PROTEIN BINDING |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 16.15 Å |
| 回转半径 Rg (电子) rg_electron | 15.87 Å |
| 零角强度 I(0) i0 | 1385120000.00 |
| 分子量 molecular_weight | 316720.0 kDa |
| 排除体积 excluded_volume | 395730 ų |
| 包络体积 envelope_volume | 29853 ų |
| 水化壳体积 shell_volume | 15288 ų |
| 包络直径 envelope_diameter | 57.7 Å |
| 壳层 Rg shell_rg | 22.35 Å |
| 包络 Rg envelope_rg | 16.93 Å |
| 形状 Rg shape_rg | 15.82 Å |
| 总 Rg total_rg | 16.13 Å |
| 总原子数 total_atoms | 43960 |
| 残基数 n_residues | 2760 |
| 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 | 53.1 Å |
| Rg (实空间) rg_real | 16.16 Å |
| Rg 误差 (实空间) rg_real_error | 0.33 Å |
| I(0) (实空间) i0_real | 1.3850e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.6580e+07 |
| Rg (倒空间) rg_reciprocal | 16.16 Å |
| I(0) (倒空间) i0_reciprocal | 1385000000.0000 |
| 解质量估计 total_estimate | 0.8775 |
| 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 | 51.7 Å |
| 偏度 Skewness skewness | 0.352 |
| 峰度 Kurtosis kurtosis | -0.344 |
| 角度范围 angular_range | — – 0.4950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 632700.0000 |
| 实空间数据点数 n_real_points | 80 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.997 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2knba_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.0 — automated matches |
| 结构域编号 domain_id | d2knbb_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.2 — SH3-domain |
| 家族 Family family | b.34.2.0 — automated matches |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 2knbA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 2knbB00 |
| 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 | 40 — SH3 Domains |