2im8
X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR213.
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 | 2im8 |
| 沉积日期 deposition_date | 2006-10-03 |
| 结构标题 title | X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR213. |
| 关键词 keywords | ;SR213, yppE, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION |
| 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 | 20.74 Å |
| 回转半径 Rg (电子) rg_electron | 19.77 Å |
| 零角强度 I(0) i0 | 15079500.00 |
| 分子量 molecular_weight | 28375.0 kDa |
| 排除体积 excluded_volume | 35115 ų |
| 包络体积 envelope_volume | 43728 ų |
| 水化壳体积 shell_volume | 18792 ų |
| 包络直径 envelope_diameter | 68.8 Å |
| 壳层 Rg shell_rg | 25.78 Å |
| 包络 Rg envelope_rg | 19.98 Å |
| 形状 Rg shape_rg | 19.77 Å |
| 总 Rg total_rg | 20.65 Å |
| 总原子数 total_atoms | 1979 |
| 残基数 n_residues | 233 |
| 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 | 67.4 Å |
| Rg (实空间) rg_real | 20.64 Å |
| Rg 误差 (实空间) rg_real_error | 0.35 Å |
| I(0) (实空间) i0_real | 1.5080e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.8180e+05 |
| Rg (倒空间) rg_reciprocal | 20.66 Å |
| I(0) (倒空间) i0_reciprocal | 15080000.0000 |
| 解质量估计 total_estimate | 0.8984 |
| 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 | 26.4 Å |
| 偏度 Skewness skewness | 0.136 |
| 峰度 Kurtosis kurtosis | -0.556 |
| 角度范围 angular_range | — – 0.3850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 4021000.0000 |
| 实空间数据点数 n_real_points | 70 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.979 |
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 | d2im8a_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.26 — YppE-like |
| 家族 Family family | a.24.26.1 — YppE-like |
| 结构域编号 domain_id | d2im8b_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.26 — YppE-like |
| 家族 Family family | a.24.26.1 — YppE-like |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 2im8A00 |
| 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 | 440 — YppE-like |
| 结构域编号 domain_id | 2im8B00 |
| 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 | 440 — YppE-like |