8g0c
Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 1 (backbone model)
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 | 8g0c |
| 沉积日期 deposition_date | 2023-01-31 |
| 结构标题 title | Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 1 (backbone model) |
| 关键词 keywords | ATP synthase, mycobacterial, inhibitor, tuberculosis, antibiotic, HYDROLASE, TRANSLOCASE-INHIBITOR complex; TRANSLOCASE/INHIBITOR |
| 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 | 63.79 Å |
| 回转半径 Rg (电子) rg_electron | 65.22 Å |
| 零角强度 I(0) i0 | 2883140000.00 |
| 分子量 molecular_weight | 279500.0 kDa |
| 排除体积 excluded_volume | 276140 ų |
| 包络体积 envelope_volume | 757210 ų |
| 水化壳体积 shell_volume | 106070 ų |
| 包络直径 envelope_diameter | 231.7 Å |
| 壳层 Rg shell_rg | 58.96 Å |
| 包络 Rg envelope_rg | 62.13 Å |
| 形状 Rg shape_rg | 65.16 Å |
| 总 Rg total_rg | 65.19 Å |
| 总原子数 total_atoms | 19874 |
| 残基数 n_residues | 4860 |
| 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 | 207.3 Å |
| Rg (实空间) rg_real | 64.50 Å |
| Rg 误差 (实空间) rg_real_error | 1.49 Å |
| I(0) (实空间) i0_real | 2.8800e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.4000e+07 |
| Rg (倒空间) rg_reciprocal | 63.00 Å |
| I(0) (倒空间) i0_reciprocal | 2875000000.0000 |
| 解质量估计 total_estimate | 0.5593 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 58.0 Å |
| 偏度 Skewness skewness | 0.587 |
| 峰度 Kurtosis kurtosis | -0.368 |
| 角度范围 angular_range | — – 0.1250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0050 |
| 最高正则化参数 α highest_alpha | 324600000.0000 |
| 实空间数据点数 n_real_points | 26 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.704; Stabil: 0.999; Sysdev: 0.004; Positv: 1.000; Valcen: 0.981; Smooth: 0.161 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (12)
6. 折叠分类 (SCOP + CATH) 29 domains
CATH v4.4 (29 domains)
| 结构域编号 domain_id | 8g0c101 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c201 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c301 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c401 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c501 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c601 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c701 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c801 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0c901 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 20 — F1FO ATP Synthase |
| 同源超家族 H-superfamily homologous superfamily | 10 — F1F0 ATP synthase subunit C |
| 结构域编号 domain_id | 8g0cA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 8g0cA02 |
| 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 | 8g0cA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 150 — Lysin |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP synthase alpha/beta chain, C-terminal domain |
| 结构域编号 domain_id | 8g0cB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 8g0cB02 |
| 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 | 8g0cB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 150 — Lysin |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP synthase alpha/beta chain, C-terminal domain |
| 结构域编号 domain_id | 8g0cC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 8g0cC02 |
| 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 | 8g0cC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 150 — Lysin |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP synthase alpha/beta chain, C-terminal domain |
| 结构域编号 domain_id | 8g0cD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 8g0cD02 |
| 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 | 8g0cD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 |
| 结构域编号 domain_id | 8g0cE01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 8g0cE02 |
| 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 | 8g0cE03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 |
| 结构域编号 domain_id | 8g0cF01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 8g0cF02 |
| 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 | 8g0cF03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 |
| 结构域编号 domain_id | 8g0cG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — ATP synthase, F1 complex, gamma subunit |
| 结构域编号 domain_id | 8g0cH01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 15 — ATP Synthase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — F0F1 ATP synthase delta/epsilon subunit, N-terminal |