2c1y
Structure of PDI-related Chaperone, Wind mutant-Y55K
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 | 2c1y |
| 沉积日期 deposition_date | 2005-09-22 |
| 结构标题 title | Structure of PDI-related Chaperone, Wind mutant-Y55K |
| 关键词 keywords | ;WIND, WINDBEUTEL, PDI-DBETA, PDI, PROTEIN DISULFIDE ISOMERASE, PIPE, DORSAL-VENTRAL PATTERNING, CHAPERONE, WIND MUTANTS, DEVELOPMENTAL PROTEIN, ENDOPLASMIC RETICULUM ;; CHAPERONE |
| 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 | 25.25 Å |
| 回转半径 Rg (电子) rg_electron | 24.54 Å |
| 零角强度 I(0) i0 | 22964300.00 |
| 分子量 molecular_weight | 37407.0 kDa |
| 排除体积 excluded_volume | 47106 ų |
| 包络体积 envelope_volume | 60725 ų |
| 水化壳体积 shell_volume | 21786 ų |
| 包络直径 envelope_diameter | 93.7 Å |
| 壳层 Rg shell_rg | 30.42 Å |
| 包络 Rg envelope_rg | 24.80 Å |
| 形状 Rg shape_rg | 24.54 Å |
| 总 Rg total_rg | 25.29 Å |
| 总原子数 total_atoms | 2649 |
| 残基数 n_residues | 359 |
| 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 | 90.2 Å |
| Rg (实空间) rg_real | 25.37 Å |
| Rg 误差 (实空间) rg_real_error | 0.75 Å |
| I(0) (实空间) i0_real | 2.2960e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.2490e+05 |
| Rg (倒空间) rg_reciprocal | 25.34 Å |
| I(0) (倒空间) i0_reciprocal | 22960000.0000 |
| 解质量估计 total_estimate | 0.8295 |
| 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 | 24.3 Å |
| 偏度 Skewness skewness | 0.468 |
| 峰度 Kurtosis kurtosis | -0.286 |
| 角度范围 angular_range | — – 0.3150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6659000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.721; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; Smooth: 0.942 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 5 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2c1ya1 |
| 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.71.1 — ERP29 C domain-like |
| 家族 Family family | a.71.1.0 — automated matches |
| 结构域编号 domain_id | d2c1ya2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.7 — ERP29 N domain-like |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 2c1yA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2c1yA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1150 — Endoplasmic reticulum protein erp29 |
| 同源超家族 H-superfamily homologous superfamily | 12 — Endoplasmic reticulum resident protein 29, C-terminal domain |
| 结构域编号 domain_id | 2c1yB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |