8oh9
Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 1)
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 | 8oh9 |
| 沉积日期 deposition_date | 2023-03-20 |
| 结构标题 title | Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 1) |
| 关键词 keywords | flavin based Electron-bifurcation, transhydrogenases, anaerobic metabolism, ELECTRON TRANSPORT; ELECTRON TRANSPORT |
| 实验方法 method | ELECTRON MICROSCOPY |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 76.13 Å |
| 回转半径 Rg (电子) rg_electron | 76.42 Å |
| 零角强度 I(0) i0 | 10363800000.00 |
| 分子量 molecular_weight | 841080.0 kDa |
| 排除体积 excluded_volume | 1042900 ų |
| 包络体积 envelope_volume | 1672600 ų |
| 水化壳体积 shell_volume | 186490 ų |
| 包络直径 envelope_diameter | 268.3 Å |
| 壳层 Rg shell_rg | 74.50 Å |
| 包络 Rg envelope_rg | 74.30 Å |
| 形状 Rg shape_rg | 76.38 Å |
| 总 Rg total_rg | 76.51 Å |
| 总原子数 total_atoms | 58132 |
| 残基数 n_residues | 7624 |
| 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 | 293.1 Å |
| Rg (实空间) rg_real | 81.34 Å |
| Rg 误差 (实空间) rg_real_error | 2.30 Å |
| I(0) (实空间) i0_real | 1.0480e+10 |
| I(0) 误差 (实空间) i0_real_error | 2.2980e+08 |
| Rg (倒空间) rg_reciprocal | 75.54 Å |
| I(0) (倒空间) i0_reciprocal | 10350000000.0000 |
| 解质量估计 total_estimate | 0.8486 |
| 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 | 83.8 Å |
| 偏度 Skewness skewness | 0.678 |
| 峰度 Kurtosis kurtosis | 0.259 |
| 角度范围 angular_range | — – 0.1050 Å−1 |
| 当前正则化参数 α current_alpha | 0.9037 |
| 最高正则化参数 α highest_alpha | 437900000.0000 |
| 实空间数据点数 n_real_points | 22 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.610; Stabil: 0.837; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.740 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 20 domains
CATH v4.4 (20 domains)
| 结构域编号 domain_id | 8oh9B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 8oh9B02 |
| 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 | 11540 — NADH-ubiquinone oxidoreductase 51kDa subunit |
| 结构域编号 domain_id | 8oh9B03 |
| 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 | 600 — |
| 结构域编号 domain_id | 8oh9B04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain |
| 结构域编号 domain_id | 8oh9B05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 8oh9E01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 8oh9E02 |
| 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 | 11540 — NADH-ubiquinone oxidoreductase 51kDa subunit |
| 结构域编号 domain_id | 8oh9E03 |
| 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 | 600 — |
| 结构域编号 domain_id | 8oh9E04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain |
| 结构域编号 domain_id | 8oh9E05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 8oh9H01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 8oh9H02 |
| 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 | 11540 — NADH-ubiquinone oxidoreductase 51kDa subunit |
| 结构域编号 domain_id | 8oh9H03 |
| 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 | 600 — |
| 结构域编号 domain_id | 8oh9H04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain |
| 结构域编号 domain_id | 8oh9H05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 8oh9K01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 8oh9K02 |
| 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 | 11540 — NADH-ubiquinone oxidoreductase 51kDa subunit |
| 结构域编号 domain_id | 8oh9K03 |
| 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 | 600 — |
| 结构域编号 domain_id | 8oh9K04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain |
| 结构域编号 domain_id | 8oh9K05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |