2csb
Crystal structure of Topoisomerase V from Methanopyrus kandleri (61 kDa fragment)
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 | 2csb |
| 沉积日期 deposition_date | 2005-05-21 |
| 结构标题 title | Crystal structure of Topoisomerase V from Methanopyrus kandleri (61 kDa fragment) |
| 关键词 keywords | ;topoisomerase IB, topoisomerase V, helix-turn-helix, helix-hairpin-helix, HhH motif, three helix bundle, Methanopyrus kandleri, ISOMERASE ;; ISOMERASE |
| 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 | 35.49 Å |
| 回转半径 Rg (电子) rg_electron | 34.81 Å |
| 零角强度 I(0) i0 | 232165000.00 |
| 分子量 molecular_weight | 119980.0 kDa |
| 排除体积 excluded_volume | 149140 ų |
| 包络体积 envelope_volume | 199000 ų |
| 水化壳体积 shell_volume | 47188 ų |
| 包络直径 envelope_diameter | 118.1 Å |
| 壳层 Rg shell_rg | 41.86 Å |
| 包络 Rg envelope_rg | 34.31 Å |
| 形状 Rg shape_rg | 34.80 Å |
| 总 Rg total_rg | 35.36 Å |
| 总原子数 total_atoms | 8411 |
| 残基数 n_residues | 1022 |
| 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 | 107.4 Å |
| Rg (实空间) rg_real | 35.38 Å |
| Rg 误差 (实空间) rg_real_error | 0.63 Å |
| I(0) (实空间) i0_real | 2.3220e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.0770e+06 |
| Rg (倒空间) rg_reciprocal | 35.45 Å |
| I(0) (倒空间) i0_reciprocal | 232200000.0000 |
| 解质量估计 total_estimate | 0.8849 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 38.2 Å |
| 偏度 Skewness skewness | 0.175 |
| 峰度 Kurtosis kurtosis | -0.626 |
| 角度范围 angular_range | — – 0.2250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 32620000.0000 |
| 实空间数据点数 n_real_points | 46 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.564 |
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 (10 domains)
| 结构域编号 domain_id | d2csba1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csba2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csba3 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csba4 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csba5 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.267 — Topoisomerase V catalytic domain-like |
| 超家族 Superfamily superfamily | a.267.1 — Topoisomerase V catalytic domain-like |
| 家族 Family family | a.267.1.1 — Topoisomerase V catalytic domain-like |
| 结构域编号 domain_id | d2csbb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.267 — Topoisomerase V catalytic domain-like |
| 超家族 Superfamily superfamily | a.267.1 — Topoisomerase V catalytic domain-like |
| 家族 Family family | a.267.1.1 — Topoisomerase V catalytic domain-like |
| 结构域编号 domain_id | d2csbb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csbb3 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csbb4 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
| 结构域编号 domain_id | d2csbb5 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.2 — RuvA domain 2-like |
| 家族 Family family | a.60.2.4 — Topoisomerase V repeat domain |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 2csbA02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 950 — |
| 结构域编号 domain_id | 2csbB02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 950 — |