1ymd
Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic form
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 | 1ymd |
| 沉积日期 deposition_date | 2005-01-20 |
| 结构标题 title | Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic form |
| 关键词 keywords | Sulfinic Cysteine, HYDROLASE, CELL CYCLE; HYDROLASE, CELL CYCLE |
| 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 | 17.15 Å |
| 回转半径 Rg (电子) rg_electron | 16.02 Å |
| 零角强度 I(0) i0 | 7459870.00 |
| 分子量 molecular_weight | 20319.0 kDa |
| 排除体积 excluded_volume | 25591 ų |
| 包络体积 envelope_volume | 29086 ų |
| 水化壳体积 shell_volume | 15270 ų |
| 包络直径 envelope_diameter | 54.0 Å |
| 壳层 Rg shell_rg | 21.94 Å |
| 包络 Rg envelope_rg | 16.36 Å |
| 形状 Rg shape_rg | 16.03 Å |
| 总 Rg total_rg | 17.05 Å |
| 总原子数 total_atoms | 1431 |
| 残基数 n_residues | 170 |
| 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 | 55.3 Å |
| Rg (实空间) rg_real | 17.07 Å |
| Rg 误差 (实空间) rg_real_error | 0.28 Å |
| I(0) (实空间) i0_real | 7.4600e+06 |
| I(0) 误差 (实空间) i0_real_error | 8.9800e+04 |
| Rg (倒空间) rg_reciprocal | 17.08 Å |
| I(0) (倒空间) i0_reciprocal | 7460000.0000 |
| 解质量估计 total_estimate | 0.8912 |
| 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 | 22.6 Å |
| 偏度 Skewness skewness | 0.200 |
| 峰度 Kurtosis kurtosis | -0.348 |
| 角度范围 angular_range | — – 0.4650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2108000.0000 |
| 实空间数据点数 n_real_points | 77 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999 |
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) 3 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1ymda2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.46 — Rhodanese/Cell cycle control phosphatase |
| 超家族 Superfamily superfamily | c.46.1 — Rhodanese/Cell cycle control phosphatase |
| 家族 Family family | c.46.1.1 — Cell cycle control phosphatase, catalytic domain |
| 结构域编号 domain_id | d1ymda3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (1 domains)
| 结构域编号 domain_id | 1ymdA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 250 — Oxidized Rhodanese; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Rhodanese-like domain |