1nbi
Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.
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 | 1nbi |
| 沉积日期 deposition_date | 2002-12-02 |
| 结构标题 title | Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM. |
| 关键词 keywords | Methyltransferase, Glycine N-methyltransferase, Catalytic mechanism, Dynamical catalysis, 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 | 36.58 Å |
| 回转半径 Rg (电子) rg_electron | 35.89 Å |
| 零角强度 I(0) i0 | 236945000.00 |
| 分子量 molecular_weight | 124050.0 kDa |
| 排除体积 excluded_volume | 154960 ų |
| 包络体积 envelope_volume | 203560 ų |
| 水化壳体积 shell_volume | 46615 ų |
| 包络直径 envelope_diameter | 108.8 Å |
| 壳层 Rg shell_rg | 43.58 Å |
| 包络 Rg envelope_rg | 34.36 Å |
| 形状 Rg shape_rg | 35.89 Å |
| 总 Rg total_rg | 36.42 Å |
| 总原子数 total_atoms | 8740 |
| 残基数 n_residues | 1100 |
| 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 | 111.7 Å |
| Rg (实空间) rg_real | 36.39 Å |
| Rg 误差 (实空间) rg_real_error | 0.74 Å |
| I(0) (实空间) i0_real | 2.3690e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.4560e+06 |
| Rg (倒空间) rg_reciprocal | 36.51 Å |
| I(0) (倒空间) i0_reciprocal | 237000000.0000 |
| 解质量估计 total_estimate | 0.9094 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 54.5 Å |
| 偏度 Skewness skewness | 0.031 |
| 峰度 Kurtosis kurtosis | -0.725 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 82130000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969 |
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) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1nbia_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.66 — S-adenosyl-L-methionine-dependent methyltransferases |
| 超家族 Superfamily superfamily | c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases |
| 家族 Family family | c.66.1.5 — Glycine N-methyltransferase |
| 结构域编号 domain_id | d1nbib_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.66 — S-adenosyl-L-methionine-dependent methyltransferases |
| 超家族 Superfamily superfamily | c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases |
| 家族 Family family | c.66.1.5 — Glycine N-methyltransferase |
| 结构域编号 domain_id | d1nbic_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.66 — S-adenosyl-L-methionine-dependent methyltransferases |
| 超家族 Superfamily superfamily | c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases |
| 家族 Family family | c.66.1.5 — Glycine N-methyltransferase |
| 结构域编号 domain_id | d1nbid_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.66 — S-adenosyl-L-methionine-dependent methyltransferases |
| 超家族 Superfamily superfamily | c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases |
| 家族 Family family | c.66.1.5 — Glycine N-methyltransferase |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1nbiA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 46 — Glycine N-methyltransferase; chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glycine N-methyltransferase, chain A, domain 1 |
| 结构域编号 domain_id | 1nbiA02 |
| 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 | 150 — Vaccinia Virus protein VP39 |
| 结构域编号 domain_id | 1nbiB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 46 — Glycine N-methyltransferase; chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glycine N-methyltransferase, chain A, domain 1 |
| 结构域编号 domain_id | 1nbiB02 |
| 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 | 150 — Vaccinia Virus protein VP39 |
| 结构域编号 domain_id | 1nbiC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 46 — Glycine N-methyltransferase; chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glycine N-methyltransferase, chain A, domain 1 |
| 结构域编号 domain_id | 1nbiC02 |
| 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 | 150 — Vaccinia Virus protein VP39 |
| 结构域编号 domain_id | 1nbiD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 46 — Glycine N-methyltransferase; chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glycine N-methyltransferase, chain A, domain 1 |
| 结构域编号 domain_id | 1nbiD02 |
| 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 | 150 — Vaccinia Virus protein VP39 |