2jdi
Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide)
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 | 2jdi |
| 沉积日期 deposition_date | 2007-01-09 |
| 结构标题 title | Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide) |
| 关键词 keywords | ATP PHOSPHORYLASE, HYDROLASE, ATP SYNTHESIS; HYDROLASE |
| 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 | 43.34 Å |
| 回转半径 Rg (电子) rg_electron | 42.68 Å |
| 零角强度 I(0) i0 | 1677760000.00 |
| 分子量 molecular_weight | 342580.0 kDa |
| 排除体积 excluded_volume | 430650 ų |
| 包络体积 envelope_volume | 555680 ų |
| 水化壳体积 shell_volume | 100760 ų |
| 包络直径 envelope_diameter | 146.7 Å |
| 壳层 Rg shell_rg | 52.99 Å |
| 包络 Rg envelope_rg | 42.70 Å |
| 形状 Rg shape_rg | 42.70 Å |
| 总 Rg total_rg | 43.03 Å |
| 总原子数 total_atoms | 24071 |
| 残基数 n_residues | 3142 |
| 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 | 134.4 Å |
| Rg (实空间) rg_real | 43.07 Å |
| Rg 误差 (实空间) rg_real_error | 0.61 Å |
| I(0) (实空间) i0_real | 1.6780e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.6930e+07 |
| Rg (倒空间) rg_reciprocal | 43.34 Å |
| I(0) (倒空间) i0_reciprocal | 1678000000.0000 |
| 解质量估计 total_estimate | 0.8793 |
| 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 | 56.0 Å |
| 偏度 Skewness skewness | 0.133 |
| 峰度 Kurtosis kurtosis | -0.374 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 344300000.0000 |
| 实空间数据点数 n_real_points | 37 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.819 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 44 domains
SCOP 2.08 (22 domains)
| 结构域编号 domain_id | d2jdia1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | a.69.1.1 — C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdia2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | b.49.1.1 — N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdia3 |
| 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.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d2jdib1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | a.69.1.1 — C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdib2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | b.49.1.1 — N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdib3 |
| 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.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d2jdic1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | a.69.1.1 — C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdic2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | b.49.1.1 — N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdic3 |
| 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.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d2jdid1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | a.69.1.1 — C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdid2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | b.49.1.1 — N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdid3 |
| 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.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d2jdie1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | a.69.1.1 — C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdie2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | b.49.1.1 — N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdie3 |
| 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.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d2jdif1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | a.69.1.1 — C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdif2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases |
| 家族 Family family | b.49.1.1 — N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 结构域编号 domain_id | d2jdif3 |
| 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.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d2jdig_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.2 — ATP synthase (F1-ATPase), gamma subunit |
| 家族 Family family | c.49.2.1 — ATP synthase (F1-ATPase), gamma subunit |
| 结构域编号 domain_id | d2jdih1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.10 — Epsilon subunit of F1F0-ATP synthase C-terminal domain |
| 家族 Family family | a.2.10.1 — Epsilon subunit of F1F0-ATP synthase C-terminal domain |
| 结构域编号 domain_id | d2jdih2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.93 — Epsilon subunit of F1F0-ATP synthase N-terminal domain |
| 超家族 Superfamily superfamily | b.93.1 — Epsilon subunit of F1F0-ATP synthase N-terminal domain |
| 家族 Family family | b.93.1.1 — Epsilon subunit of F1F0-ATP synthase N-terminal domain |
| 结构域编号 domain_id | d2jdii_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.137 — Non-globular all-alpha subunits of globular proteins |
| 超家族 Superfamily superfamily | a.137.8 — Epsilon subunit of mitochondrial F1F0-ATP synthase |
| 家族 Family family | a.137.8.1 — Epsilon subunit of mitochondrial F1F0-ATP synthase |
CATH v4.4 (22 domains)
| 结构域编号 domain_id | 2jdiA01 |
| 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 | 2jdiA02 |
| 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 | 2jdiA03 |
| 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 | 2jdiB01 |
| 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 | 2jdiB02 |
| 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 | 2jdiB03 |
| 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 | 2jdiC01 |
| 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 | 2jdiC02 |
| 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 | 2jdiC03 |
| 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 | 2jdiD01 |
| 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 | 2jdiD02 |
| 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 | 2jdiD03 |
| 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 | 2jdiE01 |
| 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 | 2jdiE02 |
| 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 | 2jdiE03 |
| 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 | 2jdiF01 |
| 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 | 2jdiF02 |
| 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 | 2jdiF03 |
| 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 | 2jdiG01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 80 — ATP synthase, gamma subunit, helix hairpin domain |
| 结构域编号 domain_id | 2jdiG02 |
| 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 | 2jdiH01 |
| 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 |
| 结构域编号 domain_id | 2jdiH02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 440 — ATP synthase delta/epsilon subunit, C-terminal domain |