1ire
Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila
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 | 1ire |
| 沉积日期 deposition_date | 2001-10-01 |
| 结构标题 title | Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila |
| 关键词 keywords | Cysteine-sulfinic acid, cysteine-sulfenic acid, post-translational modification, non-corrin cobalt, nitrile, hydration, 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 | 22.92 Å |
| 回转半径 Rg (电子) rg_electron | 21.79 Å |
| 零角强度 I(0) i0 | 41184200.00 |
| 分子量 molecular_weight | 49221.0 kDa |
| 排除体积 excluded_volume | 61359 ų |
| 包络体积 envelope_volume | 70935 ų |
| 水化壳体积 shell_volume | 26647 ų |
| 包络直径 envelope_diameter | 73.1 Å |
| 壳层 Rg shell_rg | 29.30 Å |
| 包络 Rg envelope_rg | 22.09 Å |
| 形状 Rg shape_rg | 21.78 Å |
| 总 Rg total_rg | 22.69 Å |
| 总原子数 total_atoms | 3469 |
| 残基数 n_residues | 429 |
| 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 | 72.8 Å |
| Rg (实空间) rg_real | 22.81 Å |
| Rg 误差 (实空间) rg_real_error | 0.32 Å |
| I(0) (实空间) i0_real | 4.1180e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.3450e+05 |
| Rg (倒空间) rg_reciprocal | 22.84 Å |
| I(0) (倒空间) i0_reciprocal | 41180000.0000 |
| 解质量估计 total_estimate | 0.8963 |
| 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 | 28.0 Å |
| 偏度 Skewness skewness | 0.227 |
| 峰度 Kurtosis kurtosis | -0.392 |
| 角度范围 angular_range | — – 0.3450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10560000.0000 |
| 实空间数据点数 n_real_points | 66 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.996 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 5 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1irea_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.149 — Nitrile hydratase alpha chain |
| 超家族 Superfamily superfamily | d.149.1 — Nitrile hydratase alpha chain |
| 家族 Family family | d.149.1.1 — Nitrile hydratase alpha chain |
| 结构域编号 domain_id | d1ireb_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.4 — Electron transport accessory proteins |
| 家族 Family family | b.34.4.4 — Nitrile hydratase beta chain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1ireA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 330 — Nitrile Hydratase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma |
| 结构域编号 domain_id | 1ireB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 472 — Cyclin A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Nitrile hydratase, beta subunit |
| 结构域编号 domain_id | 1ireB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 50 — |