2b0j
The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)
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 | 2b0j |
| 沉积日期 deposition_date | 2005-09-14 |
| 结构标题 title | The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd) |
| 关键词 keywords | Rossmann fold, helix bundle, OXIDOREDUCTASE; OXIDOREDUCTASE |
| 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 | 23.46 Å |
| 回转半径 Rg (电子) rg_electron | 22.58 Å |
| 零角强度 I(0) i0 | 22224200.00 |
| 分子量 molecular_weight | 37039.0 kDa |
| 排除体积 excluded_volume | 46880 ų |
| 包络体积 envelope_volume | 58975 ų |
| 水化壳体积 shell_volume | 22294 ų |
| 包络直径 envelope_diameter | 72.4 Å |
| 壳层 Rg shell_rg | 28.97 Å |
| 包络 Rg envelope_rg | 22.61 Å |
| 形状 Rg shape_rg | 22.59 Å |
| 总 Rg total_rg | 23.41 Å |
| 总原子数 total_atoms | 2593 |
| 残基数 n_residues | 344 |
| 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 | 70.9 Å |
| Rg (实空间) rg_real | 23.42 Å |
| Rg 误差 (实空间) rg_real_error | 0.43 Å |
| I(0) (实空间) i0_real | 2.2220e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.1160e+05 |
| Rg (倒空间) rg_reciprocal | 23.44 Å |
| I(0) (倒空间) i0_reciprocal | 22220000.0000 |
| 解质量估计 total_estimate | 0.9157 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 25.1 Å |
| 偏度 Skewness skewness | 0.220 |
| 峰度 Kurtosis kurtosis | -0.641 |
| 角度范围 angular_range | — – 0.3400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2887000.0000 |
| 实空间数据点数 n_real_points | 66 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.979 |
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) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2b0ja1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.11 — HMD dimerization domain-like |
| 结构域编号 domain_id | d2b0ja2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 2b0jA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 2b0jA02 |
| 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 | 1300 — Hmd, C-terminal helical subdomain |