1nbm
THE STRUCTURE OF BOVINE F1-ATPASE COVALENTLY INHIBITED WITH 4-CHLORO-7-NITROBENZOFURAZAN
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 | 1nbm |
| 沉积日期 deposition_date | 1998-04-30 |
| 结构标题 title | THE STRUCTURE OF BOVINE F1-ATPASE COVALENTLY INHIBITED WITH 4-CHLORO-7-NITROBENZOFURAZAN |
| 关键词 keywords | ATP SYNTHASE, F1FO ATP SYNTHASE, F1-ATPASE, 4-CHLORO-7-NITROBENZOFURAZAN, INHIBITION; ATP SYNTHASE |
| 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 | 41.75 Å |
| 回转半径 Rg (电子) rg_electron | 40.92 Å |
| 零角强度 I(0) i0 | 1530730000.00 |
| 分子量 molecular_weight | 325920.0 kDa |
| 排除体积 excluded_volume | 409400 ų |
| 包络体积 envelope_volume | 518920 ų |
| 水化壳体积 shell_volume | 97152 ų |
| 包络直径 envelope_diameter | 133.3 Å |
| 壳层 Rg shell_rg | 52.07 Å |
| 包络 Rg envelope_rg | 40.56 Å |
| 形状 Rg shape_rg | 40.93 Å |
| 总 Rg total_rg | 41.35 Å |
| 总原子数 total_atoms | 22893 |
| 残基数 n_residues | 2986 |
| 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 | 124.2 Å |
| Rg (实空间) rg_real | 41.44 Å |
| Rg 误差 (实空间) rg_real_error | 0.43 Å |
| I(0) (实空间) i0_real | 1.5310e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.1750e+07 |
| Rg (倒空间) rg_reciprocal | 41.74 Å |
| I(0) (倒空间) i0_reciprocal | 1531000000.0000 |
| 解质量估计 total_estimate | 0.6662 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 55.6 Å |
| 偏度 Skewness skewness | 0.015 |
| 峰度 Kurtosis kurtosis | -0.566 |
| 角度范围 angular_range | — – 0.1900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 364100000.0000 |
| 实空间数据点数 n_real_points | 39 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.955; Smooth: 0.893 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (9)
6. 折叠分类 (SCOP + CATH) 38 domains
SCOP 2.08 (19 domains)
| 结构域编号 domain_id | d1nbma1 |
| 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 | d1nbma2 |
| 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 | d1nbma3 |
| 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 | d1nbmb1 |
| 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 | d1nbmb2 |
| 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 | d1nbmb3 |
| 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 | d1nbmc1 |
| 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 | d1nbmc2 |
| 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 | d1nbmc3 |
| 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 | d1nbmd1 |
| 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 | d1nbmd2 |
| 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 | d1nbmd3 |
| 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 | d1nbme1 |
| 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 | d1nbme2 |
| 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 | d1nbme3 |
| 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 | d1nbmf1 |
| 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 | d1nbmf2 |
| 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 | d1nbmf3 |
| 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 | d1nbmg_ |
| 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 |
CATH v4.4 (19 domains)
| 结构域编号 domain_id | 1nbmA01 |
| 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 | 1nbmA02 |
| 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 | 1nbmA03 |
| 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 | 1nbmB01 |
| 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 | 1nbmB02 |
| 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 | 1nbmB03 |
| 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 | 1nbmC01 |
| 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 | 1nbmC02 |
| 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 | 1nbmC03 |
| 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 | 1nbmD01 |
| 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 | 1nbmD02 |
| 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 | 1nbmD03 |
| 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 | 1nbmE01 |
| 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 | 1nbmE02 |
| 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 | 1nbmE03 |
| 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 | 1nbmF01 |
| 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 | 1nbmF02 |
| 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 | 1nbmF03 |
| 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 | 1nbmG00 |
| 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 |