1q8j
Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+, Hcy, methyltetrahydrofolate complex)
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 | 1q8j |
| 沉积日期 deposition_date | 2003-08-21 |
| 结构标题 title | Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+, Hcy, methyltetrahydrofolate complex) |
| 关键词 keywords | homocysteine, methionine, folate, cobalamin, vitamin b12, TRANSFERASE; TRANSFERASE |
| 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 | 44.80 Å |
| 回转半径 Rg (电子) rg_electron | 45.16 Å |
| 零角强度 I(0) i0 | 215673000.00 |
| 分子量 molecular_weight | 124600.0 kDa |
| 排除体积 excluded_volume | 157860 ų |
| 包络体积 envelope_volume | 199830 ų |
| 水化壳体积 shell_volume | 41442 ų |
| 包络直径 envelope_diameter | 158.6 Å |
| 壳层 Rg shell_rg | 42.90 Å |
| 包络 Rg envelope_rg | 44.82 Å |
| 形状 Rg shape_rg | 45.14 Å |
| 总 Rg total_rg | 45.13 Å |
| 总原子数 total_atoms | 8771 |
| 残基数 n_residues | 1097 |
| 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 | 148.0 Å |
| Rg (实空间) rg_real | 45.54 Å |
| Rg 误差 (实空间) rg_real_error | 1.75 Å |
| I(0) (实空间) i0_real | 2.1570e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.9110e+06 |
| Rg (倒空间) rg_reciprocal | 44.81 Å |
| I(0) (倒空间) i0_reciprocal | 215500000.0000 |
| 解质量估计 total_estimate | 0.4635 |
| 解质量评级 solution_quality | SUSPICIOUS a SUSPICIOUS solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.6 Å |
| 偏度 Skewness skewness | 0.563 |
| 峰度 Kurtosis kurtosis | -0.551 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 25880000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.551; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.312; Smooth: 0.026 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1q8ja1 |
| 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.1.21 — Dihydropteroate synthetase-like |
| 家族 Family family | c.1.21.2 — Methyltetrahydrofolate-utiluzing methyltransferases |
| 结构域编号 domain_id | d1q8ja2 |
| 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.1.26 — Homocysteine S-methyltransferase |
| 家族 Family family | c.1.26.1 — Homocysteine S-methyltransferase |
| 结构域编号 domain_id | d1q8jb1 |
| 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.1.21 — Dihydropteroate synthetase-like |
| 家族 Family family | c.1.21.2 — Methyltetrahydrofolate-utiluzing methyltransferases |
| 结构域编号 domain_id | d1q8jb2 |
| 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.1.26 — Homocysteine S-methyltransferase |
| 家族 Family family | c.1.26.1 — Homocysteine S-methyltransferase |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1q8jA01 |
| 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 | 330 — Homocysteine-binding-like domain |
| 结构域编号 domain_id | 1q8jA02 |
| 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 | 20 — Dihydropteroate synthase-like |
| 结构域编号 domain_id | 1q8jB01 |
| 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 | 330 — Homocysteine-binding-like domain |
| 结构域编号 domain_id | 1q8jB02 |
| 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 | 20 — Dihydropteroate synthase-like |