1pcx
Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the SNARE protein Bet1
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 | 1pcx |
| 沉积日期 deposition_date | 2003-05-18 |
| 结构标题 title | Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the SNARE protein Bet1 |
| 关键词 keywords | TRANSPORT PROTEIN; TRANSPORT PROTEIN |
| 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 | 28.57 Å |
| 回转半径 Rg (电子) rg_electron | 27.52 Å |
| 零角强度 I(0) i0 | 113077000.00 |
| 分子量 molecular_weight | 84790.0 kDa |
| 排除体积 excluded_volume | 106610 ų |
| 包络体积 envelope_volume | 128880 ų |
| 水化壳体积 shell_volume | 37916 ų |
| 包络直径 envelope_diameter | 97.5 Å |
| 壳层 Rg shell_rg | 35.85 Å |
| 包络 Rg envelope_rg | 27.84 Å |
| 形状 Rg shape_rg | 27.48 Å |
| 总 Rg total_rg | 28.45 Å |
| 总原子数 total_atoms | 5952 |
| 残基数 n_residues | 753 |
| 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 | 92.2 Å |
| Rg (实空间) rg_real | 28.46 Å |
| Rg 误差 (实空间) rg_real_error | 0.59 Å |
| I(0) (实空间) i0_real | 1.1310e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.7940e+06 |
| Rg (倒空间) rg_reciprocal | 28.51 Å |
| I(0) (倒空间) i0_reciprocal | 113100000.0000 |
| 解质量估计 total_estimate | 0.8980 |
| 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 | 34.6 Å |
| 偏度 Skewness skewness | 0.188 |
| 峰度 Kurtosis kurtosis | -0.518 |
| 角度范围 angular_range | — – 0.2800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 38260000.0000 |
| 实空间数据点数 n_real_points | 57 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969 |
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) 10 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1pcxa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.71 — ERP29 C domain-like |
| 超家族 Superfamily superfamily | a.71.2 — Helical domain of Sec23/24 |
| 家族 Family family | a.71.2.1 — Helical domain of Sec23/24 |
| 结构域编号 domain_id | d1pcxa2 |
| 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.2.8 — beta-sandwich domain of Sec23/24 |
| 家族 Family family | b.2.8.1 — beta-sandwich domain of Sec23/24 |
| 结构域编号 domain_id | d1pcxa3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.62 — vWA-like |
| 超家族 Superfamily superfamily | c.62.1 — vWA-like |
| 家族 Family family | c.62.1.2 — Trunk domain of Sec23/24 |
| 结构域编号 domain_id | d1pcxa4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.109 — Gelsolin-like |
| 超家族 Superfamily superfamily | d.109.2 — C-terminal, gelsolin-like domain of Sec23/24 |
| 家族 Family family | d.109.2.1 — C-terminal, gelsolin-like domain of Sec23/24 |
| 结构域编号 domain_id | d1pcxa5 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.41 — Rubredoxin-like |
| 超家族 Superfamily superfamily | g.41.10 — Zn-finger domain of Sec23/24 |
| 家族 Family family | g.41.10.1 — Zn-finger domain of Sec23/24 |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1pcxA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 730 — Sec23/Sec24 helical domain |
| 结构域编号 domain_id | 1pcxA02 |
| 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 | 380 — Zn-finger domain of Sec23/24 |
| 结构域编号 domain_id | 1pcxA03 |
| 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 | 1670 — beta-sandwich domain of Sec23/24 |
| 结构域编号 domain_id | 1pcxA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 410 — von Willebrand factor, type A domain |
| 结构域编号 domain_id | 1pcxA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 20 — Severin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Severin |