1iv1
Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase
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 | 1iv1 |
| 沉积日期 deposition_date | 2002-03-11 |
| 结构标题 title | Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase |
| 关键词 keywords | isoprenoid, non-mevalonate, synthase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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 | 33.91 Å |
| 回转半径 Rg (电子) rg_electron | 33.61 Å |
| 零角强度 I(0) i0 | 144596000.00 |
| 分子量 molecular_weight | 97889.0 kDa |
| 排除体积 excluded_volume | 123520 ų |
| 包络体积 envelope_volume | 149330 ų |
| 水化壳体积 shell_volume | 37988 ų |
| 包络直径 envelope_diameter | 114.3 Å |
| 壳层 Rg shell_rg | 39.09 Å |
| 包络 Rg envelope_rg | 33.47 Å |
| 形状 Rg shape_rg | 33.61 Å |
| 总 Rg total_rg | 34.00 Å |
| 总原子数 total_atoms | 6912 |
| 残基数 n_residues | 900 |
| 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 | 109.4 Å |
| Rg (实空间) rg_real | 34.09 Å |
| Rg 误差 (实空间) rg_real_error | 0.96 Å |
| I(0) (实空间) i0_real | 1.4460e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1720e+06 |
| Rg (倒空间) rg_reciprocal | 33.98 Å |
| I(0) (倒空间) i0_reciprocal | 144600000.0000 |
| 解质量估计 total_estimate | 0.7809 |
| 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 | 30.3 Å |
| 偏度 Skewness skewness | 0.456 |
| 峰度 Kurtosis kurtosis | -0.548 |
| 角度范围 angular_range | — – 0.2350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 69210000.0000 |
| 实空间数据点数 n_real_points | 48 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.772; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1iv1a_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.79 — Bacillus chorismate mutase-like |
| 超家族 Superfamily superfamily | d.79.5 — IpsF-like |
| 家族 Family family | d.79.5.1 — IpsF-like |
| 结构域编号 domain_id | d1iv1b_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.79 — Bacillus chorismate mutase-like |
| 超家族 Superfamily superfamily | d.79.5 — IpsF-like |
| 家族 Family family | d.79.5.1 — IpsF-like |
| 结构域编号 domain_id | d1iv1c_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.79 — Bacillus chorismate mutase-like |
| 超家族 Superfamily superfamily | d.79.5 — IpsF-like |
| 家族 Family family | d.79.5.1 — IpsF-like |
| 结构域编号 domain_id | d1iv1d_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.79 — Bacillus chorismate mutase-like |
| 超家族 Superfamily superfamily | d.79.5 — IpsF-like |
| 家族 Family family | d.79.5.1 — IpsF-like |
| 结构域编号 domain_id | d1iv1e_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.79 — Bacillus chorismate mutase-like |
| 超家族 Superfamily superfamily | d.79.5 — IpsF-like |
| 家族 Family family | d.79.5.1 — IpsF-like |
| 结构域编号 domain_id | d1iv1f_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.79 — Bacillus chorismate mutase-like |
| 超家族 Superfamily superfamily | d.79.5 — IpsF-like |
| 家族 Family family | d.79.5.1 — IpsF-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1iv1A00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1330 — 60s Ribosomal Protein L30; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
| 结构域编号 domain_id | 1iv1B00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1330 — 60s Ribosomal Protein L30; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
| 结构域编号 domain_id | 1iv1C00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1330 — 60s Ribosomal Protein L30; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
| 结构域编号 domain_id | 1iv1D00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1330 — 60s Ribosomal Protein L30; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
| 结构域编号 domain_id | 1iv1E00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1330 — 60s Ribosomal Protein L30; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
| 结构域编号 domain_id | 1iv1F00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1330 — 60s Ribosomal Protein L30; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |