1upm
ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.
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 | 1upm |
| 沉积日期 deposition_date | 2003-10-08 |
| 结构标题 title | ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+. |
| 关键词 keywords | LYASE, CARBON-CARBON, OXIDOREDUCTASE, PHOTOSYNTHESIS, CARBON-DIOXIDE FIXATION 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 | 47.33 Å |
| 回转半径 Rg (电子) rg_electron | 46.63 Å |
| 零角强度 I(0) i0 | 4059110000.00 |
| 分子量 molecular_weight | 534410.0 kDa |
| 排除体积 excluded_volume | 667270 ų |
| 包络体积 envelope_volume | 811090 ų |
| 水化壳体积 shell_volume | 130440 ų |
| 包络直径 envelope_diameter | 138.0 Å |
| 壳层 Rg shell_rg | 60.13 Å |
| 包络 Rg envelope_rg | 46.38 Å |
| 形状 Rg shape_rg | 46.63 Å |
| 总 Rg total_rg | 46.99 Å |
| 总原子数 total_atoms | 37648 |
| 残基数 n_residues | 4712 |
| 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 | 140.0 Å |
| Rg (实空间) rg_real | 46.85 Å |
| Rg 误差 (实空间) rg_real_error | 0.64 Å |
| I(0) (实空间) i0_real | 4.0590e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.7970e+07 |
| Rg (倒空间) rg_reciprocal | 47.33 Å |
| I(0) (倒空间) i0_reciprocal | 4062000000.0000 |
| 解质量估计 total_estimate | 0.8860 |
| 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 | 63.6 Å |
| 偏度 Skewness skewness | -0.026 |
| 峰度 Kurtosis kurtosis | -0.574 |
| 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 | 3044000000.0000 |
| 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: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.828 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1upmb1 |
| 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 | d1upmb2 |
| 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 | d1upmc_ |
| 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 | d1upme1 |
| 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 | d1upme2 |
| 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 | d1upmf_ |
| 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 | d1upmh1 |
| 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 | d1upmh2 |
| 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 | d1upmi_ |
| 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 | d1upmk1 |
| 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 | d1upmk2 |
| 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 | d1upml1 |
| 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 | d1upml2 |
| 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 | d1upmm_ |
| 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 | d1upmo1 |
| 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 | d1upmo2 |
| 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 | d1upmp_ |
| 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 | d1upmr1 |
| 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 | d1upmr2 |
| 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 | d1upms_ |
| 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 | d1upmt_ |
| 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 | d1upmv1 |
| 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 | d1upmv2 |
| 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 | d1upmw_ |
| 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 | 1upmB01 |
| 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 | 1upmB02 |
| 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 | 1upmC00 |
| 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 | 1upmE01 |
| 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 | 1upmE02 |
| 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 | 1upmF00 |
| 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 | 1upmH01 |
| 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 | 1upmH02 |
| 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 | 1upmI00 |
| 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 | 1upmK01 |
| 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 | 1upmK02 |
| 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 | 1upmL01 |
| 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 | 1upmL02 |
| 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 | 1upmM00 |
| 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 | 1upmO01 |
| 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 | 1upmO02 |
| 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 | 1upmP00 |
| 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 | 1upmR01 |
| 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 | 1upmR02 |
| 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 | 1upmS00 |
| 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 | 1upmT00 |
| 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 | 1upmV01 |
| 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 | 1upmV02 |
| 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 | 1upmW00 |
| 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 |