2ipc
Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer
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 | 2ipc |
| 沉积日期 deposition_date | 2006-10-12 |
| 结构标题 title | Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer |
| 关键词 keywords | ;nucleotide binding fold, ATPase, parallel dimer, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSPORT PROTEIN ;; TRANSPORT 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 | 68.09 Å |
| 回转半径 Rg (电子) rg_electron | 68.26 Å |
| 零角强度 I(0) i0 | 2533180000.00 |
| 分子量 molecular_weight | 427620.0 kDa |
| 排除体积 excluded_volume | 536880 ų |
| 包络体积 envelope_volume | 899910 ų |
| 水化壳体积 shell_volume | 109660 ų |
| 包络直径 envelope_diameter | 220.2 Å |
| 壳层 Rg shell_rg | 70.75 Å |
| 包络 Rg envelope_rg | 65.07 Å |
| 形状 Rg shape_rg | 68.26 Å |
| 总 Rg total_rg | 68.31 Å |
| 总原子数 total_atoms | 30132 |
| 残基数 n_residues | 3746 |
| 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 | 204.3 Å |
| Rg (实空间) rg_real | 69.29 Å |
| Rg 误差 (实空间) rg_real_error | 0.65 Å |
| I(0) (实空间) i0_real | 2.4840e+09 |
| I(0) 误差 (实空间) i0_real_error | 4.5660e+07 |
| Rg (倒空间) rg_reciprocal | 67.78 Å |
| I(0) (倒空间) i0_reciprocal | 2531000000.0000 |
| 解质量估计 total_estimate | 0.6702 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 79.9 Å |
| 偏度 Skewness skewness | 0.273 |
| 峰度 Kurtosis kurtosis | -0.641 |
| 角度范围 angular_range | — – 0.1150 Å−1 |
| 当前正则化参数 α current_alpha | 2.1980 |
| 最高正则化参数 α highest_alpha | 71150000.0000 |
| 实空间数据点数 n_real_points | 24 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.999; Stabil: 0.910; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000 |
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) 12 domains
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 2ipcA01 |
| 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 | 2ipcA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1440 — Pre-protein croslinking domain of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — SecA, preprotein cross-linking domain |
| 结构域编号 domain_id | 2ipcA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3060 — Helical scaffold and wing domains of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — Helical scaffold and wing domains of SecA |
| 结构域编号 domain_id | 2ipcB01 |
| 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 | 2ipcB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1440 — Pre-protein croslinking domain of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — SecA, preprotein cross-linking domain |
| 结构域编号 domain_id | 2ipcB04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3060 — Helical scaffold and wing domains of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — Helical scaffold and wing domains of SecA |
| 结构域编号 domain_id | 2ipcC01 |
| 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 | 2ipcC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1440 — Pre-protein croslinking domain of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — SecA, preprotein cross-linking domain |
| 结构域编号 domain_id | 2ipcC04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3060 — Helical scaffold and wing domains of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — Helical scaffold and wing domains of SecA |
| 结构域编号 domain_id | 2ipcD01 |
| 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 | 2ipcD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1440 — Pre-protein croslinking domain of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — SecA, preprotein cross-linking domain |
| 结构域编号 domain_id | 2ipcD04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3060 — Helical scaffold and wing domains of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — Helical scaffold and wing domains of SecA |