1k98
AdoMet complex of MetH C-terminal fragment
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 | 1k98 |
| 沉积日期 deposition_date | 2001-10-27 |
| 结构标题 title | AdoMet complex of MetH C-terminal fragment |
| 关键词 keywords | AdoMet binding, MOTION OF 4-HELIX BUNDLE, DOMAIN INTERACTIONS, 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 | 27.42 Å |
| 回转半径 Rg (电子) rg_electron | 26.43 Å |
| 零角强度 I(0) i0 | 72075300.00 |
| 分子量 molecular_weight | 66189.0 kDa |
| 排除体积 excluded_volume | 82666 ų |
| 包络体积 envelope_volume | 100870 ų |
| 水化壳体积 shell_volume | 31855 ų |
| 包络直径 envelope_diameter | 93.6 Å |
| 壳层 Rg shell_rg | 33.76 Å |
| 包络 Rg envelope_rg | 26.60 Å |
| 形状 Rg shape_rg | 26.46 Å |
| 总 Rg total_rg | 27.07 Å |
| 总原子数 total_atoms | 4662 |
| 残基数 n_residues | 577 |
| 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 | 91.1 Å |
| Rg (实空间) rg_real | 27.43 Å |
| Rg 误差 (实空间) rg_real_error | 0.62 Å |
| I(0) (实空间) i0_real | 7.2080e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.0670e+06 |
| Rg (倒空间) rg_reciprocal | 27.43 Å |
| I(0) (倒空间) i0_reciprocal | 72080000.0000 |
| 解质量估计 total_estimate | 0.8839 |
| 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 | 31.4 Å |
| 偏度 Skewness skewness | 0.386 |
| 峰度 Kurtosis kurtosis | -0.226 |
| 角度范围 angular_range | — – 0.2900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 17070000.0000 |
| 实空间数据点数 n_real_points | 59 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.929 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1k98a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.46 — Methionine synthase domain-like |
| 超家族 Superfamily superfamily | a.46.1 — Methionine synthase domain |
| 家族 Family family | a.46.1.1 — Methionine synthase domain |
| 结构域编号 domain_id | d1k98a2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.6 — Cobalamin (vitamin B12)-binding domain |
| 家族 Family family | c.23.6.1 — Cobalamin (vitamin B12)-binding domain |
| 结构域编号 domain_id | d1k98a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.173 — Methionine synthase activation domain-like |
| 超家族 Superfamily superfamily | d.173.1 — Methionine synthase activation domain-like |
| 家族 Family family | d.173.1.1 — Methionine synthase SAM-binding domain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1k98A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 280 — Cobalamin-binding domain |
| 结构域编号 domain_id | 1k98A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 196 — Cobalamin-dependent Methionine Synthase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Vitamin B12-dependent methionine synthase, activation domain |
| 结构域编号 domain_id | 1k98A03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methionine synthase domain |
| 结构域编号 domain_id | 1k98A04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 288 — Cobalamin-dependent Methionine Synthase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cobalamin-dependent Methionine Synthase, domain 2 |