2b5m
Crystal Structure of DDB1
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 | 2b5m |
| 沉积日期 deposition_date | 2005-09-28 |
| 结构标题 title | Crystal Structure of DDB1 |
| 关键词 keywords | DDB1, beta-propeller, propeller cluster, DNA BINDING PROTEIN-PROTEIN BINDING COMPLEX; DNA BINDING PROTEIN/PROTEIN BINDING |
| 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 | 35.15 Å |
| 回转半径 Rg (电子) rg_electron | 34.34 Å |
| 零角强度 I(0) i0 | 237856000.00 |
| 分子量 molecular_weight | 124770.0 kDa |
| 排除体积 excluded_volume | 156560 ų |
| 包络体积 envelope_volume | 206010 ų |
| 水化壳体积 shell_volume | 49791 ų |
| 包络直径 envelope_diameter | 111.9 Å |
| 壳层 Rg shell_rg | 41.06 Å |
| 包络 Rg envelope_rg | 34.09 Å |
| 形状 Rg shape_rg | 34.34 Å |
| 总 Rg total_rg | 34.82 Å |
| 总原子数 total_atoms | 8768 |
| 残基数 n_residues | 1119 |
| 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 | 111.9 Å |
| Rg (实空间) rg_real | 35.06 Å |
| Rg 误差 (实空间) rg_real_error | 0.72 Å |
| I(0) (实空间) i0_real | 2.3790e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.9160e+06 |
| Rg (倒空间) rg_reciprocal | 35.12 Å |
| I(0) (倒空间) i0_reciprocal | 237900000.0000 |
| 解质量估计 total_estimate | 0.8312 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 39.8 Å |
| 偏度 Skewness skewness | 0.224 |
| 峰度 Kurtosis kurtosis | -0.540 |
| 角度范围 angular_range | — – 0.2250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 48430000.0000 |
| 实空间数据点数 n_real_points | 46 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2b5ma1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.4 — WD40 repeat-like |
| 家族 Family family | b.69.4.3 — DDB1-like |
| 结构域编号 domain_id | d2b5ma2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.4 — WD40 repeat-like |
| 家族 Family family | b.69.4.3 — DDB1-like |
| 结构域编号 domain_id | d2b5ma3 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.297 — DDB1 C-terminal-like |
| 超家族 Superfamily superfamily | a.297.1 — DDB1 C-terminal-like |
| 家族 Family family | a.297.1.1 — DDB1 C-terminal-like |
| 结构域编号 domain_id | d2b5ma4 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.4 — WD40 repeat-like |
| 家族 Family family | b.69.4.3 — DDB1-like |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2b5mA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 2b5mA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 2b5mA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 2b5mA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 910 — |