1v0y
Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.
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 | 1v0y |
| 沉积日期 deposition_date | 2004-04-02 |
| 结构标题 title | Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine. |
| 关键词 keywords | PHOSPHOLIPASE D, HYDROLASE, SUBSTRATE SOAK, DIBUTYRYLPHOSPHATIDYLCHOLINE, DIC4PC; HYDROLASE |
| 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 | 22.65 Å |
| 回转半径 Rg (电子) rg_electron | 21.47 Å |
| 零角强度 I(0) i0 | 48936500.00 |
| 分子量 molecular_weight | 53040.0 kDa |
| 排除体积 excluded_volume | 65866 ų |
| 包络体积 envelope_volume | 74127 ų |
| 水化壳体积 shell_volume | 27762 ų |
| 包络直径 envelope_diameter | 81.0 Å |
| 壳层 Rg shell_rg | 29.29 Å |
| 包络 Rg envelope_rg | 21.76 Å |
| 形状 Rg shape_rg | 21.43 Å |
| 总 Rg total_rg | 22.46 Å |
| 总原子数 total_atoms | 3729 |
| 残基数 n_residues | 493 |
| 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 | 80.1 Å |
| Rg (实空间) rg_real | 22.53 Å |
| Rg 误差 (实空间) rg_real_error | 0.64 Å |
| I(0) (实空间) i0_real | 4.8940e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.4800e+05 |
| Rg (倒空间) rg_reciprocal | 22.56 Å |
| I(0) (倒空间) i0_reciprocal | 48940000.0000 |
| 解质量估计 total_estimate | 0.7693 |
| 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 | 27.9 Å |
| 偏度 Skewness skewness | 0.206 |
| 峰度 Kurtosis kurtosis | -0.277 |
| 角度范围 angular_range | — – 0.3500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 8959000.0000 |
| 实空间数据点数 n_real_points | 67 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.668; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000 |
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) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1v0ya1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.136 — Phospholipase D/nuclease |
| 超家族 Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| 家族 Family family | d.136.1.2 — Phospholipase D |
| 结构域编号 domain_id | d1v0ya2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.136 — Phospholipase D/nuclease |
| 超家族 Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| 家族 Family family | d.136.1.2 — Phospholipase D |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1v0yA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 870 — Endonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Endonuclease Chain A |
| 结构域编号 domain_id | 1v0yA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 870 — Endonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Endonuclease Chain A |