1rco
SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE
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 | 1rco |
| 沉积日期 deposition_date | 1996-10-31 |
| 结构标题 title | SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE |
| 关键词 keywords | LYASE, CARBON-CARBON; LYASE |
| 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 | 47.24 Å |
| 回转半径 Rg (电子) rg_electron | 46.53 Å |
| 零角强度 I(0) i0 | 4043900000.00 |
| 分子量 molecular_weight | 533660.0 kDa |
| 排除体积 excluded_volume | 666530 ų |
| 包络体积 envelope_volume | 804240 ų |
| 水化壳体积 shell_volume | 129760 ų |
| 包络直径 envelope_diameter | 137.6 Å |
| 壳层 Rg shell_rg | 59.98 Å |
| 包络 Rg envelope_rg | 46.22 Å |
| 形状 Rg shape_rg | 46.53 Å |
| 总 Rg total_rg | 46.90 Å |
| 总原子数 total_atoms | 37608 |
| 残基数 n_residues | 4720 |
| 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 | 135.8 Å |
| Rg (实空间) rg_real | 46.76 Å |
| Rg 误差 (实空间) rg_real_error | 0.57 Å |
| I(0) (实空间) i0_real | 4.0440e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.8960e+07 |
| Rg (倒空间) rg_reciprocal | 47.23 Å |
| I(0) (倒空间) i0_reciprocal | 4046000000.0000 |
| 解质量估计 total_estimate | 0.8724 |
| 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 | 65.8 Å |
| 偏度 Skewness skewness | -0.027 |
| 峰度 Kurtosis kurtosis | -0.578 |
| 角度范围 angular_range | — – 0.1650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2880000000.0000 |
| 实空间数据点数 n_real_points | 34 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.552 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1rcob1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcob2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcoc_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcoe1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcoe2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcof_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcoh1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcoh2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcoi_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcok1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcok2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcol1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcol2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcom_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcoo1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcoo2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcop_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcor1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcor2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcos_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcot_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
| 结构域编号 domain_id | d1rcov1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.14 — RuBisCo, C-terminal domain |
| 家族 Family family | c.1.14.1 — RuBisCo, large subunit, C-terminal domain |
| 结构域编号 domain_id | d1rcov2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.9 — RuBisCO, large subunit, small (N-terminal) domain |
| 家族 Family family | d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase |
| 结构域编号 domain_id | d1rcow_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.73 — RuBisCO, small subunit |
| 超家族 Superfamily superfamily | d.73.1 — RuBisCO, small subunit |
| 家族 Family family | d.73.1.1 — RuBisCO, small subunit |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1rcoB01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoE01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoH01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoI00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoK01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoK02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoL01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoL02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoM00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoO01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoO02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoP00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoR01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoR02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoS00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoT00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |
| 结构域编号 domain_id | 1rcoV01 |
| 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 | 150 — RuBisCO large subunit, N-terminal domain |
| 结构域编号 domain_id | 1rcoV02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain |
| 结构域编号 domain_id | 1rcoW00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribulose bisphosphate carboxylase, small subunit |