1nbf
Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde
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 | 1nbf |
| 沉积日期 deposition_date | 2002-12-02 |
| 结构标题 title | Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde |
| 关键词 keywords | deubiquitinating enzyme, HAUSP, Ubiquitin binding, catalytic mechanisms of UPBs, HYDROLASE; HYDROLASE |
| 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 | 37.40 Å |
| 回转半径 Rg (电子) rg_electron | 36.76 Å |
| 零角强度 I(0) i0 | 288545000.00 |
| 分子量 molecular_weight | 136520.0 kDa |
| 排除体积 excluded_volume | 170510 ų |
| 包络体积 envelope_volume | 229430 ų |
| 水化壳体积 shell_volume | 52350 ų |
| 包络直径 envelope_diameter | 125.9 Å |
| 壳层 Rg shell_rg | 42.84 Å |
| 包络 Rg envelope_rg | 36.43 Å |
| 形状 Rg shape_rg | 36.77 Å |
| 总 Rg total_rg | 37.13 Å |
| 总原子数 total_atoms | 9602 |
| 残基数 n_residues | 1184 |
| 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 | 121.5 Å |
| Rg (实空间) rg_real | 37.36 Å |
| Rg 误差 (实空间) rg_real_error | 0.95 Å |
| I(0) (实空间) i0_real | 2.8850e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.8080e+06 |
| Rg (倒空间) rg_reciprocal | 37.39 Å |
| I(0) (倒空间) i0_reciprocal | 288600000.0000 |
| 解质量估计 total_estimate | 0.9010 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 40.5 Å |
| 偏度 Skewness skewness | 0.267 |
| 峰度 Kurtosis kurtosis | -0.567 |
| 角度范围 angular_range | — – 0.2100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 71650000.0000 |
| 实空间数据点数 n_real_points | 43 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.939 |
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) 10 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1nbfa_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.3 — Cysteine proteinases |
| 超家族 Superfamily superfamily | d.3.1 — Cysteine proteinases |
| 家族 Family family | d.3.1.9 — Ubiquitin carboxyl-terminal hydrolase, UCH |
| 结构域编号 domain_id | d1nbfb_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.3 — Cysteine proteinases |
| 超家族 Superfamily superfamily | d.3.1 — Cysteine proteinases |
| 家族 Family family | d.3.1.9 — Ubiquitin carboxyl-terminal hydrolase, UCH |
| 结构域编号 domain_id | d1nbfc_ |
| 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 |
| 结构域编号 domain_id | d1nbfd_ |
| 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 |
| 结构域编号 domain_id | d1nbfe_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.3 — Cysteine proteinases |
| 超家族 Superfamily superfamily | d.3.1 — Cysteine proteinases |
| 家族 Family family | d.3.1.9 — Ubiquitin carboxyl-terminal hydrolase, UCH |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1nbfA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 210 — ubp-family deubiquitinating enzyme fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ubp-family deubiquitinating enzyme superfamily |
| 结构域编号 domain_id | 1nbfB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 210 — ubp-family deubiquitinating enzyme fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ubp-family deubiquitinating enzyme superfamily |
| 结构域编号 domain_id | 1nbfC00 |
| 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 | 1nbfD00 |
| 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 | 1nbfE02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 210 — ubp-family deubiquitinating enzyme fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ubp-family deubiquitinating enzyme superfamily |