2dg1
Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus, complexed with Ca2+
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 | 2dg1 |
| 沉积日期 deposition_date | 2006-03-07 |
| 结构标题 title | Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus, complexed with Ca2+ |
| 关键词 keywords | BETA PROPELLER, HYDROLASE; HYDROLASE |
| 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 | 47.45 Å |
| 回转半径 Rg (电子) rg_electron | 47.41 Å |
| 零角强度 I(0) i0 | 657940000.00 |
| 分子量 molecular_weight | 215140.0 kDa |
| 排除体积 excluded_volume | 269760 ų |
| 包络体积 envelope_volume | 362210 ų |
| 水化壳体积 shell_volume | 64556 ų |
| 包络直径 envelope_diameter | 154.9 Å |
| 壳层 Rg shell_rg | 50.83 Å |
| 包络 Rg envelope_rg | 45.99 Å |
| 形状 Rg shape_rg | 47.42 Å |
| 总 Rg total_rg | 47.52 Å |
| 总原子数 total_atoms | 15160 |
| 残基数 n_residues | 1927 |
| 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 | 155.6 Å |
| Rg (实空间) rg_real | 47.47 Å |
| Rg 误差 (实空间) rg_real_error | 1.68 Å |
| I(0) (实空间) i0_real | 6.5790e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.2460e+07 |
| Rg (倒空间) rg_reciprocal | 47.46 Å |
| I(0) (倒空间) i0_reciprocal | 657900000.0000 |
| 解质量估计 total_estimate | 0.8801 |
| 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 | 61.3 Å |
| 偏度 Skewness skewness | 0.226 |
| 峰度 Kurtosis kurtosis | -0.610 |
| 角度范围 angular_range | — – 0.1650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 33140000.0000 |
| 实空间数据点数 n_real_points | 34 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.771 |
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) 17 domains
SCOP 2.08 (11 domains)
| 结构域编号 domain_id | d2dg1a2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.6 — Calcium-dependent phosphotriesterase |
| 家族 Family family | b.68.6.1 — SGL-like |
| 结构域编号 domain_id | d2dg1a3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2dg1b2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.6 — Calcium-dependent phosphotriesterase |
| 家族 Family family | b.68.6.1 — SGL-like |
| 结构域编号 domain_id | d2dg1b3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2dg1c_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.6 — Calcium-dependent phosphotriesterase |
| 家族 Family family | b.68.6.1 — SGL-like |
| 结构域编号 domain_id | d2dg1d2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.6 — Calcium-dependent phosphotriesterase |
| 家族 Family family | b.68.6.1 — SGL-like |
| 结构域编号 domain_id | d2dg1d3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2dg1e2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.6 — Calcium-dependent phosphotriesterase |
| 家族 Family family | b.68.6.1 — SGL-like |
| 结构域编号 domain_id | d2dg1e3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2dg1f2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.6 — Calcium-dependent phosphotriesterase |
| 家族 Family family | b.68.6.1 — SGL-like |
| 结构域编号 domain_id | d2dg1f3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2dg1A00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 30 — TolB, C-terminal domain |
| 结构域编号 domain_id | 2dg1B00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 30 — TolB, C-terminal domain |
| 结构域编号 domain_id | 2dg1C00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 30 — TolB, C-terminal domain |
| 结构域编号 domain_id | 2dg1D00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 30 — TolB, C-terminal domain |
| 结构域编号 domain_id | 2dg1E00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 30 — TolB, C-terminal domain |
| 结构域编号 domain_id | 2dg1F00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 30 — TolB, C-terminal domain |