1lwt
Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)
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 | 1lwt |
| 沉积日期 deposition_date | 2002-06-03 |
| 结构标题 title | Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free) |
| 关键词 keywords | HOMING ENDONUCLEASE, PROTEIN-DNA COMPLEX, INTEIN, ENDONUCLEASE, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA |
| 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 | 31.42 Å |
| 回转半径 Rg (电子) rg_electron | 30.30 Å |
| 零角强度 I(0) i0 | 125671000.00 |
| 分子量 molecular_weight | 73471.0 kDa |
| 排除体积 excluded_volume | 85159 ų |
| 包络体积 envelope_volume | 113000 ų |
| 水化壳体积 shell_volume | 32829 ų |
| 包络直径 envelope_diameter | 119.8 Å |
| 壳层 Rg shell_rg | 35.25 Å |
| 包络 Rg envelope_rg | 30.56 Å |
| 形状 Rg shape_rg | 30.24 Å |
| 总 Rg total_rg | 30.84 Å |
| 总原子数 total_atoms | 5050 |
| 残基数 n_residues | 514 |
| 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 | 112.2 Å |
| Rg (实空间) rg_real | 31.69 Å |
| Rg 误差 (实空间) rg_real_error | 1.45 Å |
| I(0) (实空间) i0_real | 1.2570e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.3820e+06 |
| Rg (倒空间) rg_reciprocal | 31.58 Å |
| I(0) (倒空间) i0_reciprocal | 125700000.0000 |
| 解质量估计 total_estimate | 0.6182 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 110.0 Å |
| 偏度 Skewness skewness | 0.578 |
| 峰度 Kurtosis kurtosis | 0.015 |
| 角度范围 angular_range | — – 0.2500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10480000.0000 |
| 实空间数据点数 n_real_points | 51 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.869; Smooth: 0.755 |
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) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1lwta1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.86 — Hedgehog/intein (Hint) domain |
| 超家族 Superfamily superfamily | b.86.1 — Hedgehog/intein (Hint) domain |
| 家族 Family family | b.86.1.2 — Intein (protein splicing domain) |
| 结构域编号 domain_id | d1lwta2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.95 — Homing endonuclease-like |
| 超家族 Superfamily superfamily | d.95.2 — Homing endonucleases |
| 家族 Family family | d.95.2.2 — Intein endonuclease |
| 结构域编号 domain_id | d1lwta3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.95 — Homing endonuclease-like |
| 超家族 Superfamily superfamily | d.95.2 — Homing endonucleases |
| 家族 Family family | d.95.2.2 — Intein endonuclease |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1lwtA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 16 — Endonuclease - Pi-scei; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hedgehog/Intein (Hint) domain |
| 结构域编号 domain_id | 1lwtA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 28 — Endonuclease I-creI |
| 同源超家族 H-superfamily homologous superfamily | 10 — Homing endonucleases |
| 结构域编号 domain_id | 1lwtA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 28 — Endonuclease I-creI |
| 同源超家族 H-superfamily homologous superfamily | 10 — Homing endonucleases |