1oqy
Structure of the DNA repair protein hHR23a
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 | 1oqy |
| 沉积日期 deposition_date | 2003-03-11 |
| 结构标题 title | Structure of the DNA repair protein hHR23a |
| 关键词 keywords | DNA repair, proteasome-mediated degradation, protein-protein interaction, REPLICATION; REPLICATION |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 69.79 Å |
| 回转半径 Rg (电子) rg_electron | 69.83 Å |
| 零角强度 I(0) i0 | 3392020000.00 |
| 分子量 molecular_weight | 474260.0 kDa |
| 排除体积 excluded_volume | 587220 ų |
| 包络体积 envelope_volume | 1269700 ų |
| 水化壳体积 shell_volume | 152530 ų |
| 包络直径 envelope_diameter | 248.4 Å |
| 壳层 Rg shell_rg | 68.13 Å |
| 包络 Rg envelope_rg | 68.74 Å |
| 形状 Rg shape_rg | 69.85 Å |
| 总 Rg total_rg | 69.70 Å |
| 总原子数 total_atoms | 65808 |
| 残基数 n_residues | 4356 |
| 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 | 245.9 Å |
| Rg (实空间) rg_real | 72.86 Å |
| Rg 误差 (实空间) rg_real_error | 1.26 Å |
| I(0) (实空间) i0_real | 3.3970e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.6100e+07 |
| Rg (倒空间) rg_reciprocal | 69.92 Å |
| I(0) (倒空间) i0_reciprocal | 3393000000.0000 |
| 解质量估计 total_estimate | 0.8981 |
| 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 | 78.2 Å |
| 偏度 Skewness skewness | 0.524 |
| 峰度 Kurtosis kurtosis | 0.139 |
| 角度范围 angular_range | — – 0.1100 Å−1 |
| 当前正则化参数 α current_alpha | 1.0860 |
| 最高正则化参数 α highest_alpha | 525300000.0000 |
| 实空间数据点数 n_real_points | 23 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.814; Stabil: 0.885; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.643 |
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 | d1oqya1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.5 — RuvA C-terminal domain-like |
| 超家族 Superfamily superfamily | a.5.2 — UBA-like |
| 家族 Family family | a.5.2.1 — UBA domain |
| 结构域编号 domain_id | d1oqya2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.5 — RuvA C-terminal domain-like |
| 超家族 Superfamily superfamily | a.5.2 — UBA-like |
| 家族 Family family | a.5.2.1 — UBA domain |
| 结构域编号 domain_id | d1oqya3 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.189 — XPC-binding domain-like |
| 超家族 Superfamily superfamily | a.189.1 — XPC-binding domain |
| 家族 Family family | a.189.1.1 — XPC-binding domain |
| 结构域编号 domain_id | d1oqya4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1oqyA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 1oqyA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ubiquitin-associated (UBA) domain |
| 结构域编号 domain_id | 1oqyA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 540 — XPC-binding domain |
| 结构域编号 domain_id | 1oqyA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ubiquitin-associated (UBA) domain |