1svd
The structure of Halothiobacillus neapolitanus RuBisCo
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 | 1svd |
| 沉积日期 deposition_date | 2004-03-29 |
| 结构标题 title | The structure of Halothiobacillus neapolitanus RuBisCo |
| 关键词 keywords | beta-alpha-barrel, LYASE; 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 | 26.41 Å |
| 回转半径 Rg (电子) rg_electron | 25.89 Å |
| 零角强度 I(0) i0 | 63761300.00 |
| 分子量 molecular_weight | 62165.0 kDa |
| 排除体积 excluded_volume | 77604 ų |
| 包络体积 envelope_volume | 93040 ų |
| 水化壳体积 shell_volume | 30146 ų |
| 包络直径 envelope_diameter | 91.7 Å |
| 壳层 Rg shell_rg | 33.07 Å |
| 包络 Rg envelope_rg | 26.42 Å |
| 形状 Rg shape_rg | 25.90 Å |
| 总 Rg total_rg | 26.60 Å |
| 总原子数 total_atoms | 4385 |
| 残基数 n_residues | 553 |
| 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 | 87.2 Å |
| Rg (实空间) rg_real | 26.45 Å |
| Rg 误差 (实空间) rg_real_error | 0.63 Å |
| I(0) (实空间) i0_real | 6.3760e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.4570e+05 |
| Rg (倒空间) rg_reciprocal | 26.44 Å |
| I(0) (倒空间) i0_reciprocal | 63760000.0000 |
| 解质量估计 total_estimate | 0.8855 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.1 Å |
| 偏度 Skewness skewness | 0.410 |
| 峰度 Kurtosis kurtosis | -0.270 |
| 角度范围 angular_range | — – 0.3000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 21840000.0000 |
| 实空间数据点数 n_real_points | 61 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.955 |
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) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1svda1 |
| 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 | d1svda2 |
| 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 | d1svdm1 |
| 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 (3 domains)
| 结构域编号 domain_id | 1svdA01 |
| 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 | 1svdA02 |
| 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 | 1svdM00 |
| 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 |