1pda
STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE
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 | 1pda |
| 沉积日期 deposition_date | 1992-11-17 |
| 结构标题 title | STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE |
| 关键词 keywords | PORPHYRIN, 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 | 20.26 Å |
| 回转半径 Rg (电子) rg_electron | 19.21 Å |
| 零角强度 I(0) i0 | 19151000.00 |
| 分子量 molecular_weight | 32439.0 kDa |
| 排除体积 excluded_volume | 40411 ų |
| 包络体积 envelope_volume | 46768 ų |
| 水化壳体积 shell_volume | 20433 ų |
| 包络直径 envelope_diameter | 65.2 Å |
| 壳层 Rg shell_rg | 25.34 Å |
| 包络 Rg envelope_rg | 19.24 Å |
| 形状 Rg shape_rg | 19.22 Å |
| 总 Rg total_rg | 20.01 Å |
| 总原子数 total_atoms | 2278 |
| 残基数 n_residues | 296 |
| 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 | 62.8 Å |
| Rg (实空间) rg_real | 20.17 Å |
| Rg 误差 (实空间) rg_real_error | 0.29 Å |
| I(0) (实空间) i0_real | 1.9150e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.3740e+05 |
| Rg (倒空间) rg_reciprocal | 20.19 Å |
| I(0) (倒空间) i0_reciprocal | 19150000.0000 |
| 解质量估计 total_estimate | 0.9060 |
| 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 | 23.3 Å |
| 偏度 Skewness skewness | 0.203 |
| 峰度 Kurtosis kurtosis | -0.451 |
| 角度范围 angular_range | — – 0.3900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6586000.0000 |
| 实空间数据点数 n_real_points | 71 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.995 |
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 | d1pdaa1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.94 — Periplasmic binding protein-like II |
| 超家族 Superfamily superfamily | c.94.1 — Periplasmic binding protein-like II |
| 家族 Family family | c.94.1.1 — Phosphate binding protein-like |
| 结构域编号 domain_id | d1pdaa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.50 — dsRBD-like |
| 超家族 Superfamily superfamily | d.50.2 — Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain |
| 家族 Family family | d.50.2.1 — Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1pdaA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1pdaA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1pdaA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 160 — Double Stranded RNA Binding Domain |
| 同源超家族 H-superfamily homologous superfamily | 40 — Porphobilinogen deaminase, C-terminal domain |