1xdt
COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
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 | 1xdt |
| 沉积日期 deposition_date | 1997-11-18 |
| 结构标题 title | COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR |
| 关键词 keywords | ;COMPLEX (TOXIN-GROWTH FACTOR), DIPHTHERIA TOXIN, RECEPTOR, HEPARIN-BINDING EPIDERMAL GROWTH FACTOR, EPIDERMAL GROWTH FACTOR, COMPLEX (TOXIN-GROWTH FACTOR) complex ;; COMPLEX (TOXIN/GROWTH FACTOR) |
| 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 | 29.69 Å |
| 回转半径 Rg (电子) rg_electron | 28.82 Å |
| 零角强度 I(0) i0 | 62154700.00 |
| 分子量 molecular_weight | 61159.0 kDa |
| 排除体积 excluded_volume | 76284 ų |
| 包络体积 envelope_volume | 99035 ų |
| 水化壳体积 shell_volume | 28712 ų |
| 包络直径 envelope_diameter | 91.2 Å |
| 壳层 Rg shell_rg | 36.18 Å |
| 包络 Rg envelope_rg | 28.15 Å |
| 形状 Rg shape_rg | 28.79 Å |
| 总 Rg total_rg | 29.65 Å |
| 总原子数 total_atoms | 4306 |
| 残基数 n_residues | 559 |
| 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 | 86.1 Å |
| Rg (实空间) rg_real | 29.56 Å |
| Rg 误差 (实空间) rg_real_error | 0.49 Å |
| I(0) (实空间) i0_real | 6.2150e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.7930e+05 |
| Rg (倒空间) rg_reciprocal | 29.62 Å |
| I(0) (倒空间) i0_reciprocal | 62160000.0000 |
| 解质量估计 total_estimate | 0.8996 |
| 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 | 45.5 Å |
| 偏度 Skewness skewness | 0.019 |
| 峰度 Kurtosis kurtosis | -0.834 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11180000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.764 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1xdtr_ |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.3 — Knottins (small inhibitors, toxins, lectins) |
| 超家族 Superfamily superfamily | g.3.11 — EGF/Laminin |
| 家族 Family family | g.3.11.1 — EGF-type module |
| 结构域编号 domain_id | d1xdtt1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f |
| 超家族 Superfamily superfamily | b.2.1 — Diphtheria toxin, C-terminal domain |
| 家族 Family family | b.2.1.1 — Diphtheria toxin, C-terminal domain |
| 结构域编号 domain_id | d1xdtt2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.166 — ADP-ribosylation |
| 超家族 Superfamily superfamily | d.166.1 — ADP-ribosylation |
| 家族 Family family | d.166.1.1 — ADP-ribosylating toxins |
| 结构域编号 domain_id | d1xdtt3 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.1 — Toxins' membrane translocation domains |
| 超家族 Superfamily superfamily | f.1.2 — Diphtheria toxin, middle domain |
| 家族 Family family | f.1.2.1 — Diphtheria toxin, middle domain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1xdtR00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 25 — Laminin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Laminin |
| 结构域编号 domain_id | 1xdtT01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 175 — Diphtheria Toxin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Diphtheria Toxin, domain 1 |
| 结构域编号 domain_id | 1xdtT02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 490 — Globin-like |
| 同源超家族 H-superfamily homologous superfamily | 40 — Diphtheria toxin, translocation domain |
| 结构域编号 domain_id | 1xdtT03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 700 — Diphtheria toxin, receptor-binding domain |