1gl9
Archaeoglobus fulgidus reverse gyrase complexed with ADPNP
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 | 1gl9 |
| 沉积日期 deposition_date | 2001-08-30 |
| 结构标题 title | Archaeoglobus fulgidus reverse gyrase complexed with ADPNP |
| 关键词 keywords | TOPOISOMERASE, DNA SUPERCOILING, ARCHAEA, HELICASE; TOPOISOMERASE |
| 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 | 46.99 Å |
| 回转半径 Rg (电子) rg_electron | 47.05 Å |
| 零角强度 I(0) i0 | 770655000.00 |
| 分子量 molecular_weight | 232640.0 kDa |
| 排除体积 excluded_volume | 293040 ų |
| 包络体积 envelope_volume | 426000 ų |
| 水化壳体积 shell_volume | 76595 ų |
| 包络直径 envelope_diameter | 182.0 Å |
| 壳层 Rg shell_rg | 50.37 Å |
| 包络 Rg envelope_rg | 46.50 Å |
| 形状 Rg shape_rg | 47.05 Å |
| 总 Rg total_rg | 47.18 Å |
| 总原子数 total_atoms | 16398 |
| 残基数 n_residues | 2025 |
| 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 | 171.0 Å |
| Rg (实空间) rg_real | 47.16 Å |
| Rg 误差 (实空间) rg_real_error | 2.08 Å |
| I(0) (实空间) i0_real | 7.7070e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.5570e+07 |
| Rg (倒空间) rg_reciprocal | 46.99 Å |
| I(0) (倒空间) i0_reciprocal | 770500000.0000 |
| 解质量估计 total_estimate | 0.8441 |
| 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 | 55.3 Å |
| 偏度 Skewness skewness | 0.500 |
| 峰度 Kurtosis kurtosis | 0.065 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 67030000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.686; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.914 |
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) 22 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1gl9b1 |
| 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.37.1.16 — Helicase-like domain of reverse gyrase |
| 结构域编号 domain_id | d1gl9b2 |
| 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.37.1.16 — Helicase-like domain of reverse gyrase |
| 结构域编号 domain_id | d1gl9b3 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.10 — Prokaryotic type I DNA topoisomerase |
| 超家族 Superfamily superfamily | e.10.1 — Prokaryotic type I DNA topoisomerase |
| 家族 Family family | e.10.1.1 — Prokaryotic type I DNA topoisomerase |
| 结构域编号 domain_id | d1gl9c1 |
| 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.37.1.16 — Helicase-like domain of reverse gyrase |
| 结构域编号 domain_id | d1gl9c2 |
| 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.37.1.16 — Helicase-like domain of reverse gyrase |
| 结构域编号 domain_id | d1gl9c3 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.10 — Prokaryotic type I DNA topoisomerase |
| 超家族 Superfamily superfamily | e.10.1 — Prokaryotic type I DNA topoisomerase |
| 家族 Family family | e.10.1.1 — Prokaryotic type I DNA topoisomerase |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 1gl9B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 20 — Anthopleurin-A |
| 同源超家族 H-superfamily homologous superfamily | 30 — reverse gyrase domain |
| 结构域编号 domain_id | 1gl9B02 |
| 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 | 1gl9B03 |
| 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 | 1gl9B04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — |
| 结构域编号 domain_id | 1gl9B05 |
| 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 | 140 — |
| 结构域编号 domain_id | 1gl9B06 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 460 — Topoisomerase I; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Topoisomerase I, domain 2 |
| 结构域编号 domain_id | 1gl9B07 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 510 — EV matrix protein fold |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1gl9B08 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 290 — Topoisomerase I; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Topoisomerase I, domain 4 |
| 结构域编号 domain_id | 1gl9C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 20 — Anthopleurin-A |
| 同源超家族 H-superfamily homologous superfamily | 30 — reverse gyrase domain |
| 结构域编号 domain_id | 1gl9C02 |
| 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 | 1gl9C03 |
| 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 | 1gl9C04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — |
| 结构域编号 domain_id | 1gl9C05 |
| 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 | 140 — |
| 结构域编号 domain_id | 1gl9C06 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 460 — Topoisomerase I; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Topoisomerase I, domain 2 |
| 结构域编号 domain_id | 1gl9C07 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 510 — EV matrix protein fold |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1gl9C08 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 290 — Topoisomerase I; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Topoisomerase I, domain 4 |